BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS Pages 496-503

Vol. 180, No. 2, 1991 October 31, 1991

INHIBITORY BINDING THE DNA PRIMER

Kalman

OF ADENOSINE DIPHOSPHORIBOSYLTRANSFERASE SITE OF REVERSE TRANSCRIPTASE TEMPI~ATES

G.

Buki,

Pal

I.

Bauer

and

Ernest

TO

Kun*

L a b o r a t o r y for E n v i r o n m e n t a l T o x i c o l o g y and Chemistry, and the Octamer Research Foundation, Romberg Tiburon Centers, S a n F r a n c i s c o State University, Tiburon, CA 94920

Received September 9, 1991

Purified adenosine d i p h o s p h o r i b o s e t r a n s f e r a s e protein binds to RNA-DNA hybrid templates of reverse t r a n s c r i p t a s e at the DNA p r i m e r s i t e and i n h i b i t s RT a c t i v i t y of H I V and M M u RTs. T h i s action is p r e v e n t e d by a u t o - p o l y - A D P - r i b o s y l a t i o n of the transferase but is reinduced by inhibitory ligands of the enzyme. © ~991 Academic Press, Inc.

Adenosine diphosphoribosyl

transferase

(ADPRT, E.C.2.4.2.30)

highly abundant non-histone nuclear protein of higher and

there

is

synthesizing

convincing

function of

evidence this

that

protein

the

oligo(ADP-ribose)

synthesis

represents

only

a

few

(1,2).

This is

of the D N A - i n d e p e n d e n t

rates of

(3), which

even in the 56 kDa p o l y p e p t i d e

eukaryotes

poly(ADP-ribose)

p e r c e n t of its m o l e c u l a r activity in intact cells in a g r e e m e n t with the m a g n i t u d e

is a

can be readily

fragment of ADPRT

determined

(4) that has no

DNA r e c o g n i t i o n sites

(5). C o n s e q u e n t l y the r e l a t i v e l y slow auto-

poly-ADP-ribosylation

of A D P R T

in

intact

cells

function

by

covalently

to

the

ADPRT

the b i n d i n g

DNA r e g i o n s

topological

serves

providing bound

demonstrating internal

(6)

changes

and slow t u r n o v e r

most

probably

(ADPR)n

Considerable (I0,ii),

from the binding

that

evidence

of A D P R T to DNA t e r m i n i

and c r u c i f o r m DNA result

a self-regulatory

DNA-repelling (7).

of the p o l y m e r

as well

is

exists as to

and s i g n i f i c a n t

of ADPRT

to circular

To whom correspondence should be addressed. ADPRT, A d e n o s i n e d i p h o s p h o r i b o s y l transferase; RT, r e v e r s e t r a n s c r i p t a s e ; TE, T r i s - E D T A buffer; NA, n u c l e i c acid; GSH, reduced glutathione; DTT, dithiothreitol; (ADPR)n , polyadenosine diphosphoribose; MMu RT, Moloney murine leucosis virus RT. Abbreviations:

0006-291X/91 $1.50 Copyright © 1991 by Academic Press, Inc. All rights of reproduction in any form reserved.

496

Vol. 180, No. 2, 1991

DNA,

a process

inhibitory

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

that

ligands

has a regulatory has

also

Klenow

been

(12).

also

regulated

Recently, that

is i n h i b i t e d

by a u t o - A D P - r i b o s y l a t i o n

The p r e s e n t with

the

primer

report,

binding

shown

(8),

DNA

and

(28), and it

synthesis

and

this

enzyme

that A D P R T by the

inhibition

of ADPRT or by removal

to R N A - D N A

sites of reverse transcriptase M~terials

NAD

of Zn 2+

(9).

as an e x t e n s i o n

of A D P R T

both

of SV40 DNA

in v i t r o

by A D P R T

from one of its two zinc fingers

by

it has been

effect on the synthesis

demonstrated

fragment

modulated

is

of p r e v i o u s hybrids,

studies,

deals

in p a r t i c u l a r

to

templates.

and M e t h o d s

MMu RT, p ( r A ) . ( d T ) 1 2 _ 1 8 and p( rC) . (dG)l 2-1 8 w e r e o b t a i n e d from Pharmacia (Piscataway, NJ), and polyA (average length of 300 b), h i s t o n e s (Cat. #7755), oligo(dT) 12,18, d G T ~ 5 and TTP frp~ Sigma (St. Louis, MO). Trac~ nucleot-ides [ ~ - ~ P ] T T P , [a-JzP]dGTP (each 650 Ci/mmol) and [ P]NAD (250 Ci/mmol) were purchased from ICN (Irvine, CA). ADPRT was prepared from calf thymus by a published method (14). HIV reverse transcriptase (recombinant, clone BH-10) was a gift from the AIDS R e s e a r c h and R e f e r e n c e R e a g e n t P r o g r a m of AIDS, NIAID, NIH (Rockville, MD). O c t a m e r i c d s D N A (GCATGCAT) was p r e p a r e d by a n n e a l i n g s y n t h e t i c c o m p l e m e n t i n g s t r a n d s (15). C o e n z y m i c DNA (CoDNA) c o n s i s t e d of 2 0 0 - 1 0 0 0 bp dsDNA, a s i d e p r o d u c t of the i s o l a t i o n of A D P R T (13), w i t h an average of 500 bp (325 kDa) size. Nitrocellulose membranes (type HA, 2.4 cm d i a m e t e r , 0 . 4 5 ~m) w e r e from M i l l i p o r e (Bedford, MA) and filter b i n d i n g assays were p e r f o r m e d as p u b l i s h e d (12). The labeled hybrid polynucleotide p(rA).p([32p]dT) was p r e p a r e d by a n n e a l i n g 66 ~ g of poly(rA) w i t h 0.8 ~ g oligo(dT) 1 2 _ 1 8 in 40 ~ i of TE buffer at room temperature for 30 min, then 200 ~ i of 5xHIV buffer (25~^mM Tris-HCl, 300 mM KCl, 35 mM MgCl2, pH 8.2) and 70 ~ C i of [e-~zP]TTP and 650 ~ i of sterile water were added. Finally 0.5 ~ g of H I V - R T in i00 ~ i of RT d i l u t e r (50 mM p h o s p h a t e , pH 7.2, 50 mM KCl, 50% glycerol and 0.2% Triton X-100) was admixed and the system incubated at 25°C for 40 min, followed by extraction w i t h phenol/chloroform, 1 : l(v/v) and w i t h chloroform. The nucleic acid was precipitated with 2 volumes of 100% ethanol o v e r n i g h t at -20°C, c e n t r i f u g e d and the p r e c i p i t a t e dissolved in 40 ~ i of TE buffer. Spectrophotometric assay for nucleic acid c o n c e n t r a t i o n was based on 1 A260 = 40 ~ g n u c l e i c acid, and the specific activity was 28,500 cpm/~g. Gel retardation was assayed in b o t h 1.2% a g a r o s e and 4% a c r y l a m i d e gels as d e s c r i b e d (16). A s s a y s for A D P R T a c t i v i t y were done in a l i q u o t s (50 ~I) containing 16.5 pmol of ADPRT in IxHIV buffer supplemented with 8 mM DTT, 2 mM GSH, and 0.i mM [32p]NAD (0.i ~ C i ) . After incubation at 2 5 ° C for 4 min, t h e r e a c t i o n w a s s t o p p e d by 2 ml of 20% t r i c h l o r o a c e t i c acid and the precipitate collected by filtration and r a d i o a c t i v i t y c o u n t e d by liquid s c i n t i l l a t i o n s p e c t r o m e t r y (13). The A D P - r i b o s y l a t e d ADPRT was made in 6 ml of reaction mix c o n t a i n i n g 25 mM Tris. HCl (pH7.7), 1 mM EDTA, 0,25 mM NAD, 0.2% Tween 20, 240 ~ g of A D P R T and 0.i ~ g of o c t a m e r i c dsDNA. A f t e r incubation for 2 h o u r s at 25°C, the m i x w a s c o n c e n t r a t e d in C e n t r i c o n 30 (Amicon, Beverly, MA) to 3 m g / m l and the m e d i u m changed to 25 mM Tris.HCl (pH 7.7), 1 mM EDTA, I0 mM 2-mercaptoe t h a n o l , 0 . 2 % T w e e n 20 with the concomitant r e m o v a l of t h e o c t a m e r i c DNA and NAD. HIV RT a c t i v i t y was a s s a y e d in 50 ~ i of 497

Vol. 180, No. 2, 1991

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

i x H I V b u f f e r s u p p l e m e n t e d w i t h 8 mM DTT, 2 m M GSH, 50 )/M [uzP]TTP or [a-JZ]dGTP and 2 //g of p ( r A ) . (dT) 1 2 - 1 8 or p(rC). ( d G ) 1 2 _ 1 8 ; 0.03 lag of H I V RT s t a r t e d p o l y m e r i z a t i o n at 25°C, w h i c h was s t o p p e d a f t e r i0 min w i t h cold TCA, p r e c i p i t a t e c o l l e c t e d on f i l t e r s , and r a d i o a c t i v i t y c o u n t e d as for A D P R T assays above. In experiments (Fig. 3B, 4B), where the concentrat i o n of (dT) 12_18 p r i m e r was varied, the poly(rA) was kept cons t a n t ( 3 . 3 ) a g / t u b e ) a n d a n n e a l i n g w a s a l l o w e d for 30 m i n at ambient temperature in TE b u f f e r p r i o r to a d d i t i o n of o t h e r components of the RT assay. With MMu RT, the reaction was done at 37°C. RNase H activity was tested as p u b l i s h e d (17) and partially z i n c - d e p l e t e d ADPRT was prepared as reported (9).

Results

Binding constants hybrid

were

of A D P R T

determined

system containing tions

by a filter b i n d i n g

1.5 nM A D P R T

of the hybrid between

analysis for

and HIV RT to the p o l y ( r A ) . (dT) 12_18 technique

or HIV RT and v a r y i n g

0.075 and 3 ~g/ml.

r e v e a l e d h i g h a f f i n i t y K d values,

ADPRT

and

0.31

±

0.i

nM

for

HIV

in a

concentra-

Scatchard binding

namely

RT,

(12)

as

0.26 ± 0.I nM

determined

in

5

parallel tests.

Binding of A D P R T to the hybrid nucleic acid was also d e m o n s t r a t e d with the gel r e t a r d a t i o n the

retardation

tions its

of the

of ADPRT,

substrate

When

the

(18)

(Fig.

labeled

whereas

i.)

hybrid

preincubation

- completely

enzymatic

benzamide

assay

abolished

activity

The

by

first

increasing

of A D P R T

with

retardation

of A D P R T

5 lines show

was

by

-

6-10). either

(19) A D P R T was

bound to the hybrid as shown by u n i m p a i r e d r e t a r d a t i o n 20).

1 mM NAD

(lanes

inhibited

or 5 - i o d o - 6 - a m i n o - l , 2 - b e n z o p y r o n e

concentra-

(lanes Ii-

It was d e t e r m i n e d

in separate tests that b e n z a m i d e at 0.4 mM

or 5 - I - l , 2 - b e n z o p y r o n e

at 0.5 mM had no direct effect on isolated

RT enzymes hybrid

(not shown).

(not shown).

HIV RT also retarded the m i g r a t i o n of the

Since binding of ADPRT to DNA termini

gene-

rally increases the p o l y m e r a s e activity of ADPRT,

we compared the

coenzymatic

activators

ADPRT, (15).

function

coenzymic Results

are

DNA

of

the

(14)

hybrid

with

and a s y n t h e t i c

illustrated

in Fig.

2

known

octameric wherein

it is e v i d e n t

that despite the strong b i n d i n g of the hybrid to ADPRT, small c o e n z y m a t i c

activation

of

DNA d u p l e x

of the p o l y ( A D P - r i b o s e )

only very polymerase

function of ADPRT is conferred by the hybrid. The s u p p r e s s i v e effect of ADPRT on HIV RT activity is illustrated in Fig.3 show

a

(A and B). Two different templates were used and results stronger

suppression

with

498

p(rA). (dT)12_18

than

with

Vol. 1 80, No. 2, 1991

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

60 ~

O CoDNA oe%amer

50 --

/

40 o o .~

30

0

20

I

10

Origin --

300 bp --

,-, I

0

10-+ 10-~ 10-2 10-1 100 101 102 10~

(9

1 2 3 4 5 6 7 8 910111213141516171819~

~.~

nucleic a c i d , nM

F i g u r e I % Gel r e t a r d a t i o n a s s a y for t h e b i n d i n g of A D P R T to p(rA}.p([~ZP]dT) hybrid polynucleotide. Gel: 1.2% agarose. NA: 35 ng (1000 cpm)/lane, Lanes 1-5 show the retardation of labeled hybrid NA by increasing amounts (0, 5, 10, 20, 40 ng) of ADPRT. (Note: due to a handling error, lane 4 contained 40 ng and lane 5 20 ng of ADPRT) Lanes 6-10 are with the same p r o g r e s s i o n of ADPRT amounts but preincubated with 1 mM NAD for i0 min at ambient temp; lanes 11-15 are the same but with benzamide added (0.4 mM); while lanes 16-20 have 5-iodo-6-amino-l,2-benzopyrone (0.5mM) added. Fiqure 2. Coenzymic activity of CoDNA, octameric deoxyrlbonucleotide duplex (octamer DNA) and p(rA). (dT)12_18 on the rates of auto-poly-ADP-ribosylation of ADPRT. Assay for ADPRT activity described in Methods.

p(rC). (dG)12_18; slightly binding

above

HIV

RT

by

hybrid.

ADPRT

action

of A D P R T

(compare

inhibitory Zn 2+

(9),

of

ADPRT

parable

to

the

its

RT

inhibitory enzyme

0.3

latter

template.

two

by

diminishes

RT

but

HIV

RT

(Fig.

of

partial

effect The

on

the

effect

DNA of

499

of

presumably site the

second

of

a the

inhibitory curve

from

inhibitory

action

Poly-ADP-ribosylated

ADPRT

(Fig.

does

of

obtained

of inhibition

3B),

with

and

preference

primer

no d i r e c t

former

results

reinforce

4A),

pretreatment

influence

(9).

the

compare

have

The

with

(Fig.

for

curves).

on H I V

ADPRT,

to

3B;

the

kinetics

that histones of

for

agrees

ADPRT

themselves

action

~M

competition

and

lower

from

binding

Klenow

is

The apparent

(top c u r v e

has

benzopyrone

(i0).

histones

RT

of

the

is of i n t e r e s t

whereas

no

ADPRT

simulates

on H I V

tion

for

between

It

of

to p ( r A ) . ( d T ) 1 2 _ 1 8

dsDNAs

competition

top)

1 ~M

of A D P R T

with various

I50

not

and

with abolish

4B) . T h e s e zinc

the

on

MMu

deple-

inhibitory

results

depletion

polymerase ADPRT

partial

6-nitroso-l,2-

of

activity RT

are

com-

ADPRT of

activity

on the is

Vol.

180,

No.

2, 1 9 9 1

BIOCHEMICAL

AND

BIOPHYSICAL

A

RESEARCH COMMUNICATIONS

B

100 oiodG emplte05

/

° r1406°0°4 p(rA).oUgo(dT)ternpla'~teI ~ .

20

0.2

--

0.1

0 0.01

........

I 0. I

........

I I

i

i -200

0

ADPRT concentration (/~M)

200

l 600

400

i/[prirner],

800

I000

/~M-*

F i q u r e 3. A: T h e inhibitory e f f e c t of A D P R T on HIV RT at v a r y i n g c o n c e n t r a t i o n s o f A D P R T w i t h t w o t y p e s o f R N A - D N A h y b r i d s as t e m p l a t e s . H u n d r e d % a c t i v i t i e s w e r e 53 p m o l a n d 21 p m o l of n u c l e o t i d e s incorporated for the A.T and C.dG templates respectiv e l y , a n d 3 jsg h i s t o n e s were present in a l l a s s a y s . B: L i n e w e a v e r - B u r k p l o t of H I V R T a c t i v i t y at v a r y i n g c o n c e n t r a t i o n s of p r i m e r . Ordinate ( l / V ) is in u n i t s of pmol-" of TMP i n c o r p o r a t e d in 10 min. 0, no a d d i t i v e ; V , p l u s h i s t o n e s (3 Jug) ; • , plus ADPRT (0.67 JuM) ; ¥ , plus histones and ADPRT.

summarized

in T a b l e

inhibitory

action

tory,

and

i. of

preference

Just

as w i t h

HIV

ADPRT

without

being

of

p(rA).(dT)12_18

A

B

100 - o

| 0.2 ~-

RT,

histones

by to

promote

themselves

p(rC).(dG)12_18

~ NOBP-treatedADPRT • ADPRT

/

"--o ~

8o

O

~

60



4-0

~

2o

0.1 O

L

0

0.01

O ADP-rlbosylated

--



• native

,

,

i ,,,,,[

i

,

, ,lJl,[

0.1

1

-200

ADPRT, /~M

0

200

400

1/[primer],

600

800 -1

1000

/~M

Figure 4. A : T h e e f f e c t of native A D P R T a n d of a u t o - A D P - r i b o s y l a t e d A D P R T o n H I V R T activity. C o n d i t i o n s w e r e the same as in Fig. 3A, a u t o - A D P - r i b o s y l a t e d ADPRT was made as d e s c r i b e d in Methods, 100% activity: 65 pmoles TMP incorporated. B: The effects on H I V R T a c t i v i t y of n a t i v e A D P R T and A D P R T w h i c h is 50% z i n c - d e p l e t e d b y t r e a t m e n t w i t h 6 - n i t r o s o - l , 2 - b e n z o p y r o n e (NOBP). C o n d i t i o n s were the same as in Fig. 3B.

500

the

inhibiwas

Vol. 180, No. 2, 1991

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Table

1

The effect of ADPRT on the activity of MMu RT RT activity with Exper. conditions

p(rC)-(dG)I2-18

No ADPRT,

120 (100%)

+ ADPRT,

No Histone No Histone

No ADPRT, + ADPRT,

p(rA)-(dT)I2_I8

81 (38% inhib.)

+ Histone

109

+ Histone

56.8

(100%)

12.9

(87% inhib.)

58.2

30 (75% inhib.)

6.7

(88% inhib.)

RT concentration was 0.02 ~g/test consisting of ~ m M Tris-HCl ~ H 8.5 at 25~C), 8 mM SgCl2, i0 mM DDT, 0.5 mM [ ~ - ~ P ] T T P or [aP]dGTP, 1 ~ g of p(rA). (dT)12_18 or p(rC). (dG)12_18 in 50 ~i volume. ADPRT: 0.67 uM; histones: 5 ~g/test, if present. Incubation was carried out at 37°C for 5 min and acid p r e c i p i t a b l e radioactive product assayed as described in Methods. Values in the table are given as pmoles of deoxyribonucleotides incorporated in 5 min at 37°C. Data are the averages of 3 parallel assays, not differing more than ±10% from the mean value.

also

shown.

its R N a s e

Contrary

H activity

to

was

the

DNA

synthetic

activity

by ADPRT

(results

unaffected

of

HIV

RT,

n o t shown).

Discussion The

inhibitory

site

of R T

template

DNA

hybrids.

has

only

adds per

effect

to a l r e a d y

which

we

probably

observe ADPRT

1 ~M

Therefore

ADPRT

to

RT

relevance. nuclear the

cytosol

species lase

templates

(27)

cellular

(21)

(22).

of A D P R T (23-26) in

range

conclude

within

However

the

were

isolated

antiretroviral

cell

evidence

identified

may

RT

RT

as w e l l

is a selfof A D P R T

are

well

at

within

which

binding

is of

pharmacological

is a p r e d o m i n a n t l y

is m a i n l y that

as

properties

in nuclei,

have

inasmuch

of A D P R T

501

observation

a drug-induced

exists

ribonucleoprotein action

of

acid

in p h y s i o l o g i c a l l y

that ADPRT

retroviral

is n o t e x c l u s i v e ,

This

formation

existing

to R N A -

nucleic

concentrations

that

thought

whereas

(ADPR)n

The

of A D P R T

colligative role

inhibition

concentration

It is g e n e r a l l y

enzyme

lization

ADPRT.

we

that

at t h e p r i m e r

hybrid

ADPRT.

a prominent

enzymatic

significant

the actual (20).

of

the

on

evidence

play

binding

binding,

efficacy

and that

activity

on D N A s y n t h e s i s

a novel

strong

coenzymic

cells

regulatory

the

accumulating

s_ee of A D P R T

functioning

illustrates

Despite

minimal

of A D P R T

the

operative

in

nuclear

loca-

as c y t o p l a s m i c

ADPRT

(ADPR) n g l y c o h y d r o -

particles. ligands,

which

Therefore may

a

induce

Vol. 180, No. 2, 1991

the

binding

example

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

of A D P R T

of which

to

RT

is reported

templates,

cannot

in an accompanying

be

excluded,

paper

an

(19).

Acknowledgments This r e s e a r c h was s u p p o r t e d by A F O S R 8 9 - 0 2 3 1 and by funds of O c t a m e r R e s e a r c h Foundation. The f o l l o w i n g r e a g e n t was o b t a i n e d t h r o u g h the AIDS R e s e a r c h and R e f e r e n c e R e a g e n t Program, NIAID, NIH: H I V r e v e r s e t r a n s c r i p t a s e f r o m the Univ. of A l a b a m a at Birmingham, Center for AIDS Res., Gene Expression Core Facility.

References

i. 2. 3. 4.

5. 6. 7. 8. 9. i0. ii. 12. 13. 14. 15. 16.

17. 18. 19. 20.

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Inhibitory binding of adenosine diphosphoribosyl transferase to the DNA primer site of reverse transcriptase templates.

Purified adenosine diphosphoribose transferase protein binds to RNA-DNA hybrid templates of reverse transcriptase at the DNA primer site and inhibits ...
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