BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
Vol. 160, No. 3, 1989
Pages 1117-1123
May 15, 1989
INITIATION OF TRANSCRIPTION
OF rDNA IN RICE
K.Nandabalan and J.D.Padayatty
C e n t e r for Genetic E n g i n e e r i n g and D e p a r t m e n t of B i o c h e m i s t r y I n d i a n I n s t i t u t e of S c i e n c e B a n g a l o r e - 5 6 0 012, I n d i a Received March 17, 1989
Three direct repeats of 320, 340 and 238 n u c l e o t i d e s were detected u p s t r e a m to t h e 5' end of t h e 185 rRNA gene of an rDNA u n i t p r e s e n t on a 9.8 k b EcoRl f r a g m e n t of the r i c e D N A . The p r i m e r extension a n a l y s i s showed that the s i t e of i n i t i a t i o n of t r a n s c r i p t i o n i s i n t h e 1st r e p e a t at an A, t h e 623rd n u c l e o t i d e u p s t r e a m to t h e 5' end of t h e 18S rRNA gene. Different stretches of the i n t e r g e n i c s p a c e r DNA l i n k e d to t h e C h l o r a m p h e n i c o l a c e t y l t r a n s f e r a s e gene were t r a n s c r i b e d i n t h e i n t a c t n u c l e i of r i c e ~ e m b r y o s . The 51 n u c l e a s e p r o t e c t i o n z a n a l y s i s of t h e transcripts u s i n g [v P ] - l a b e l l e d Chloramphenicol acetyl t r a n s f e r a s e gene as t h e p r o b e s h o w e d the p r e s e n c e of m u l t i p l e p r o m o t e r s for F D N A transcription. ~ 1 9 8 9 A c a d e m i c Press, Inc. SUMMARY:
The all
other
rDNA i s to
genes
the
at even
for
the
eukaryotes, transcribed
185,
are
as
origin
between
transcription
of
are
start
the
identification
point
and
the rice v a r i e t y
related
located
the
promoters
the
of of
the
the
site
in
long
with
the
precrusor repeats for
of
rDNAs
species
within
long
25S
rRNAs
+20
to
rRNA in
initiation
the
plants,
repeats
like (1).
in The
initiation occurring upstream (IGS). show
(2).
in
tandem
intergenic spacer
transcription
closely
and
arranged
a single unit
18S rRNA gene i n
the
5.8S
The
Nucleotide
very
sequences
little
homology
promoters
for
the
rDNA
-150
nucleotides,
the
+1
being
(3).
In
IGS
of
of
this an
transcription
study, rDNA of
we
report
unit,
spacer
the
rDNA
in
IR20.
MATERIALS AND METHODS
S1 n u c l e a s e p r o t e c t i o n a s s a y This was done a c c o r d i n g to a m o d i f i c a t i o n (4) of t h e of H a r r i n g t o n and C h i k a r a i s h i ( 5 ) . Primer extension analysis Primer extension anaylsis was done according to the of T u r n b o u g ~ 9 et a l . ( 6 ) . N u c l e a r RNA (10 pg) (4) was m i x e d ng of 5 ' - [ ~" ~ - - 1 a-b-elled 15- met universal primer and 50 ng ABBREVIATIONS
: CAT-Chloramphenicol
acetyl
transferase;
method
method with 3 of the
IGS-Intergenic
spacer. 0006-291X/89 $1.50 1117
Copyright © 1989 by Academic Press, Inc. All rights of reproduction in any form reserved.
Vol. t60, No. 3, 1989
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
recombinant single stranded DNA bearing the insert, hybridized in 25 pl of 20 mM Tris-HCl, pH 8.0, 0.I M NaCI, 0.i mM EDTA at 60°C for 4 hr. Then, it was cooled to room temperature, 25 pl of the buffer containing 0.i M Tris-HCl, pH 8.0, I mM each of dATP, dCTP, dGTP, dTTP and 10 units of reverse transcriptase were added and incubated at 37°C for i hr. The extended products were precipitated with ethanol, dissolved in 80% formamide containing i0 mM NaOH, 1 mM EDTA, 0.025% Xylene cyanol and 0.025% Bromophenol blue, heated at 90°C for 3 min, chilled in ice and analysed on a sequencing gel, where the same insert DNA was sequenced. rDNA-Chloramphenicol acetyl transferase (CAT) gene constructs The RF DNA from the Ml3mpl8 or Ml3mpl9 clones bearing the 3.3 kb EcoRI-BamHI, the 0.35 kb BamHI or the 0.6 kb .B.amHI-SacI fragment covering the IGS of the rDNA "unit was prepared and digested with EcoRI and HindIII to release the fragments bearing the inserts. The 35SCATpUCI3 plasmid (7) (supplied by Nam-Hai Chua, Rockefeller University, New York) was restricted with BamHI and HindIII, the 0.8 kb fragment was separated by agarose gel electrophoresis and eluted. The HindIII-BamHI 0.8 kb fragment contained only the structural gene for CAT. The DNA fragments from the IGS were ligated to the 0.8 kb HindIII-BamHI fragment bearing the CAT gene and cloned at the EcoRI-BamHI sites in pBR322. Transcription in intact nuclei Transcription in intact nuclei was carried out by a modification of the method of Jost et al. (8). Nuclei (i0 O.D. units at 260 nm) isolated from 24 hr germinated rice embryos (4) were suspended in i00 pl of i0 mM Hepes, pH 7.9, 75 mM KCI, 0.5 mM dithiothreitol, i0 mM creatine phosphate and 20% glycerol. It was frozen in liquid nitrogen, thawed in ice, plasmid DNA (i pg), 600 pM each of ATP, CTP, GTP and UTP and i0 units of RNasin were added and incubated at 26°C for i hr with or without ~-Amanitin (0.5 ~g). The nuclei were then lysed with 0.5% SDS, deproteinized, and the nucleic acids were precipitated with ethanol. The DNA was then removed by digestion w i t h DNaseI (10 pg) a t 37°C for 2 h r and t h e RNA was d e p r o t e i n i z e d and p r e c i p i t a t e d w i t h e t h a n o l .
RESULTS AND DISCUSSION
Sequence of t h e IGS u p s t r e a m to the i8S rRNA gene By
screening
with
[32p]
unit
was
protection 3.3
and
the
and/or (9).
of
of
gene
sizes
by
and
the is
320,
1482
read
obtained
kb
at
from the
published
genes
the
sequence
340
nucleotides
rDNA
by
$1
nuclease
(data
not
shown).
analysis
BamHI-SacI
cloned
dideoxy
chain
termination
in
the
IGS
(Fig.2).
the
18S The of
starting
upstream The
rRNA IGS three from
the
rRNAs,
were
presence
1118
phage
fragments
(10).
by
238
the
of
[32p]
4 the
( F i g . 1)
0.35 k b BamHI, 0 . 6 k b
ladders
characterized and
with
Charon
containing
mapped
sequence
the
end
)t
insert
were
HindIII,
by
DNA i n
kb
fragments
nucleotides
5'
rice 9.8
restriction
sequenced
of
was
a
nucleotide
1.9
SacI-BamHl
sequence
gene
that
rRNA
kb
rRNA
restriction
and
of
bearing
The
EcoRI-BamHI,
0.7
library
clone
the
analyses
kb
nucleotides to
of
M13mp19 A
rRNA
EcoRI
a
obtained.
hybridization
The
an
rRNAs,
in
to
was
upstream long
of
18S 86
identical
to
the
direct
526th
method the
sequence
gene
the
M13mp18
18S
repeats
nucleotide
Vol. 160, No. 3, 1989
EcoRl
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
Hindl[l
Hindlll
BamHI Sacl
C[al
BamHl
BgIll BamHI EcoRI
J.
185
0 255
6
5.85
~
q
(
I
255
9.8 kb
v//1//i~ v/zz////J
i
i
CAT
v//////zA
FiR.l: Organization of rRNA genes, s e q u e n c i n g s t r a t e g y and t h e CAT c o n s t r u c t s . The r e s t r i c t i o n fragment was cloned in M13mp18 or M13mp19, transfected into E.coli MvIIg0, grown, the recombinant phage was prepared, single stranded DNA was i s o l a t e d and s e q u e n c e d a c c o r d i n g to the dideoxy chain termination method. The d i r e c t i o n and e x t e n t of t h e n u c l e o t i d e s e q u e n c e o b t a i n e d a r e i n d i c a t e d . The rDNA-CAT c o n s t r u c t s were made as described under Materials and Methods. The hatched a r e a r e p r e s e n t s t h e CAT gene. The i n i t i a t i o n of t r a n s c r i p t i o n i s m a r k e d b y an a r r o w ( F i g . 2 ) .
upstream
to
and
3rd,
76,
83
and
repeats the
5'
end
of
2rid
and
3rd
120
the
Within
near each
nucleotides
10096
rRNA are
However, homology,
repeat long,
i8S
repeats
6496 r e s p e c t i v e l y .
display
ends.
about
the and
there which
8ene.
the while
is by
The
ist
homologous
a
to
central
duplication
2nd,
of
occur
conserved could
1st
extent
region
variations highly
and the
of
these towards
block have
of
given
CGTGTAGGATCAGATG•ACAATACGGAAACAGACGGAAATTAGTTGCCCATTTGACAAAGCGCGATGTATTTCGCCTTGTTTTTGGCCTGGAATGCTTCG
-- 760
GATCTCTTGATCGTATA~CGCTCCTCAACGATGCCGATATAGCCGGCCAACAGCTTAATTG~TTTGCGTCCCGGTGTGGTG~TCCTTGCGGGGTTCGAGA
-- 660
GAAGGGAAATGTTGCTAGTACGGT~GAAGCTTGAGTGGAGGCACCGATGTGATGAAATTGCTACGCGAACGGGACGGTGGTGCATCTAACCTTACACGG $ 3 •GGAAAGGATTGAAAGGTTGGTA•GGGA••GTTT•AAGGAAAGTGCACCTGACAAAGCGCGGTGTTTTTCGC•TTGTTTT•GACCTGGAATGCTTCGGAT
--560
CCCTTAAACGCATACCGCACCTAAATGATGCCGGTATAGCCGGCCAACAGCTTAATTGCTTTGCGTACCCGGTGTAGCTCGCTTCG~GGGGTCTCCGAGA
-- 360
GAAGGGTAGATCTTGGTCAGTCAGTACGGTC~GAGCTCTGAGGGTGGAGGCTCACTGAGTGGTGGACTGG~ACTGAAAGTAAGCCTGGCCTACGCCCCTT
-- 260
-- 460
GAAATGGTTCAGGCGCCCAACA•ATGATCCAACAACCTGGCGCGTGGCAAGGATTGAGAGGTTGGTACGAGGCCCGTTTAAGGAAAGTGGCCG•CCTCTG --160 2 Ba,mHl ACGAAGGCGCGGTGTTGTTCGCCTTGTTTTCAACTCTGAATGCTTGGGATCCCTTGATCGTATAACGCCCTCAACGATGCCGATATAGC•GGCCAACAGC -- 60 TTAATTG~TTTGCGTCCCGGTGTG~TCCTTGGGGGGTTCGAGAGAAGGGAAATGTTGGTAGTACGGTC~GAGCTTGAGTGGAGGCACTGATGTGATGAAA +
40
GTAACTGGC•ACGC•C•TTGAAATGGTTCATGTG•CCATCACTT•GATTCCAACAACGCTTACAGTGGACCTCGATCATCGTCTTATAGCAGACCCACTT #140 I CGTAAGCAAGGTGGGATGTTTGAACGGCTTTGGTCGTTGTGGTG•GTGAGAAGCTATGGACATTGATTGCTCCGGAGGCCCCCCGTTGTTGAGCGGCCGA + 240 CTCTCGGGACTGTCATTTCAATCAAGAAATA•CGGTTTTGTACTTGTTCCCCCTCAGGAAGTGCTTGCGTTCTTCTACCCGTTATGCG•GAAGTTGATGC + 340
TTGCA•AGATTGCCTTTGTCGC•TACACCCTTGGCGTGTC•TGTCGCCACATA•CATGATAGTGTGCCTGTGTGTCGGCTAAACCGGCATCACCCAGGAC
5~cl
-I-440
ACATGTCTCTTGCCATTGGTCTCGGATGACGCTTGTATGCGAG•TCGTGGTCCTTTCGACGTGCCTCACAAAAGTTCCGTCGGAATTAATTGACG•TTGG -]-540 CTCGGCTGCCTTGAATGTTTTAGAGCATGGCCTCTGAGCTACGATTGGTAGCCTGCTGCCAACTTGTCAATGAGGAC•TTGCTACCTGGTTGATC•TGC• + 6 4 0 AGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATTGTGCAAGTATGAACTAATTGAACTGTGAA+
708
Fi~.2. N u c l e o t i d e s e q u e n c e of the IGS. The 5' end of t h e 185 rRNA gene and t h e IGS u p s t r e a m to i t w e r e s e q u e n c e d ( F i g . i ) , and a s e q u e n c e of 1568 n u c l e o t i d e s was r e a d from t h e l a d d e r s . The 185 rRNA gene i s m a r k e d b y a wavy l i n e , the repeats are underlined, the highly c o n s e r v e d r e g i o n s in t h e r e p e a t s are o v e r l i n e d , t h e p u t a t i v e p r o m o t e r and t h e p r o m o t e r l i k e s e q u e n c e s a r e b o x e d and t h e t r a n s c r i p t i o n i n i t i a t i o n s i t e i s m a r k e d b y an a r r o w , w h i c h i s t h e +1 n u c l e o t i d e . 1119
Vol. 160, No. 3, 1989
rise
to
in
the
the
longer
region
repeats
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
In
downstream
to
upstream
to
present
in the
repeats.
rDNA r e p e a t
length
rice
and
the
wheat
25S
the
rRNA
18S
(11)
the
gene
rRNA
repeats
(4)
differ
gene.
i n r i c e may be a t t r i b u t e d
The
present from
the
heterogeneity
to e i t h e r
the
differing
n u m b e r of r e p e a t s or to the p r e s e n c e of d i f f e r e n t k i n d s of r e p e a t s .
I n i t i a t i o n of rDNA t r a n s c r i p t i o n The
0.6
hybridized nuclear and a
size
3'end
to
the
18S
1st
repeat
gene.
kb
an
A,
(12) within
and
initiation There
between
(16),
(5),
an
starts in
A,
(Fig.2) A
+32
to
G.
and
In
of
dyad
of
the
-168
as
(unpublished
stem
and
the
all
maize,
of
the and
structure by
the
The
of
In
of
symmetry
the
and the of
rDNA (15) the
mouse
melanogaster
(5)
initiates where
it
rDNA t r a n s c r i p t i o n
+9 to -35
nucleotides
transcription
200
of
(15),
always
nucleotides
in
rice.
the
dominant
nucleotides
spanning
of
is
Zuker
transcription could
of
radish
transcription
rat
for
the
0.35
crustacean
start
radish
and
insert
The
BamHI-SacI
Drosophila
rDNA the
initiation
dyad
(11), or
programme
the
kb
region
(17)
140
'fold'
0.6
the
18S PRNA
transcription
promoter
for
about
with
transcription
wheat,
the
method.
before
(18)
obtained upstream
within
to
(14),
the
human
with
of
is
the
promoter
symmetry,
region
of
radish
the
data).
the maize
wheat
cases,
the
the
analyzing
was
initiates
product.
in
(14),
case
secondary
(20)
in
homology
comparison
predicted
also,
maize
the
constitute
(13) while
Xenopus l a e v i s
almost in
extended
transcription
much
(17),
laevis,
may
feature
in
a X.
region
rice
except
with
mouse,
not
to
by
nucleotide
upstream
was
and
transcriptase
product
624th
extension
upstream
fly
long
hybridizing
primer
M13mpl8
primer
determined
the
nucleotides
primer
rDNA
at
in
reverse
transcription
the
repeat
for
human
However,
with
1st
was
initiation
any
was
molecules
by
Tse-tse
the site
623
immediately
yield
T
the
precursor detected
fragment not
is
using
nucleotide
the
cloned universal
by
product
A 179
which
be
initiates
(19).
gene.
rRNA
Artemia
rat
(Fig.3).
Thus,
did
repeats.
extended
rRNA
fragment
the
gel
(Fig.l) 15-mer
extended
with
not
BamHl
the
was
corresponded
at
could
primer
of
Shorter
DNA
fragment
5'-[32p]-labelled
The
sequencing
whose
BamHI-SacI
the
RNA.
the
on
kb
to
and
occurs
possibly
play
Steigler in a
the role
i n t h e i n i t i a t i o n of t r a n s c r i p t i o n .
M u l t i p l e p r o m o t e r s for rDNA t r a n s c r i p t i o n The
3.3
rDNA-CAT of
the
kb
EcoRI-BamHI,
constructs,
358 p r o m o t e r ,
0.35
kb
BamHI and
(Fig.l),
the
and
CAT gene i n pBR322
the
CAT gene
1120
in
the
pUC13 were
0.6
kb
under used
BamHI-SacI
the
influence
as
templates
Vol. 160, No. 3, 1989
A
C
G
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
T
1
1
2
3
4
5
kb
Q b
Q
Q
Fig.3. The site of initiation of rDNA transcription. by the primer extension analysis as described Methods. Lane l-the primer extended product.
This under
was determined Materials and
Fig.4. The SI nuclease protection ~analysis of the transcripts from the rDNA-CAT constructs. The 3 ' [ ~Zp ]_labelled 0.8 kb HindIII-BamHI fragment bearing the CAT gene was hybridized to the transcripts of the rDNA-CAT constructs, digested with S1 nuclease and the protected fragments were analysed by a 8 M urea-5~ PAGE using HaeIII fragments of ~ x174 RF DNA as size markers. Protected DNA fragments from : Lane i - CAT gone with the 35S promoter in pUCI3; 2-CAT gene in pBR322 ; 3-3.3 kb EcoRI-BamHI-CAT construct ; 4-0.35 kb BamHI-CAT c o n s t r u c t , and 5-0.6 k b BamHI-SacI-CAT c o n s t r u c t .
for
transcription
to
the
the
358CATpUCI3
3
' -
[ 32p ]
in end DNA,
intact
nuclei.
labelled bearing
0.8 the
CAT 1121
The
transcripts
kb
HindIII-BamHI gene,
digested
were
hybridized
fragment, with
$I
from nuclease
Vol. 160, No. 3, 1989
and
the
the
2)
protected
rDNA-CAT
0.8
kb
fragments
constructs
fragment
showed
the
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
that
the
which
protected
the
produced
transcripts
the
CAT
gene
indicating
the
that
there
of
the
the
rDNA
control
were
rDNA
of
in
present
further
of
that
the
dyad
been
presence the
this
in
spacer
the
decreased may
to
be the
serve
the
repeats
be
around
as
of
in
The
rice
(23)
efficiency a
are
when
sink
of for
and
of
mouse
sequences may
also
promoters mouse
have
(24).
The
hypothesis
in
through
be
initiation
sequences
genes
eukaryotes enhancement'
( 25 ).
In
X.
laevis
termination
of
the
tandem
transcription the
under
faithful
the
s u p p o r t s the
'read
IGS
melanogaster and
which
for like
recycled
premature
gene
like
those
rRNA
the
control
Spacer
rDNA
repeated
factors
and
promoter
X.laevis
in
D.
promoter
data).
the
the
responsible
the
shown) showed
CAT
of
protected
not
Transient
under
constructs
results
transcription
spacer
(Fig.2)
also
(data
the
while,
transcripts
which
These
(21).
a m e c h a n i s m known as
true
not
cells
(lane
transcribed,
rDNA-CAT
rDNA
(22).
tandemly
transcription
proved
promoters
of
did
All the
band
produced
the
rRNAs.
sequences
case
promoters
not
any
~ -Amanitin
rDNA
(unpublished
through
the
was
repeats
regions
transcription
which
in
may
is
PAGE.
protected
of
plasmids carrying
Drosophila
3rd
which
All
of
for
reported
symmetry
may b e e n h a n c e d in
promoters
and
The
1).
of
upstream
M urea-5~
35S p r o m o t e r
plasmid
been
2nd
pBR322
35S-CAT
cultured
8
absence
transcription
heterologous
detected of
the
has
transcription.
exhibit also
the
the
presence
promoter
in
The
(lane
Recombinant
the
promoters
present
the
multiple
of
in
gene
in
while
transcribed
expression
CAT
unit.
3-5).
gene
by
transcripts
i n f l u e n c e of the
specific
are
lanes
CAT the
analysed
produced
(Fig.4,
CAT gene u n d e r
were
transcription
(25).
The
factors
spacer and
thus
e n h a n c e t h e t r a n s c r i p t i o n of rDNA. ACKNOWLEDGMENTS
This work was supported by the grant No.SP/SO/D83/86 from the D e p a r t m e n t of Science and T e c h n o l o g y , G o v e r n m e n t of I n d i a . The C e n t e r for Genetic E n g i n e e r i n g was e s t a b l i s h e d by the D e p a r t m e n t of B i o t e c h n o l o g y , G o v e r n m e n t of I n d i a . REFERENCES
1. A p p e l s , R . and H o n e y c u t t , R . L . (1986). In DNA s y s t e m a t i c s ( S . K . D u t t a , E d . ) , V o l . I I , p p . 8 1 - 1 3 5 . CRC P r e s s , F l o r i d a . 2. Kohorn, B.D. and Rae, P.M.M. (1982) Proc. Natl. Acad. Sci. USA, 79, 1501-1505. 3. S o l l n e r - W e b b , B. and Tower, J. (1986) A n n . R e v . B i o c h e m . 55, 801-830. 4. N a n d a b a l a n , K. and Padayatty, J.D. (1988) Biochem. Biophys. Res. Comm. 157, 68-74. 5. H a r r i n g t o n , C.A. and C h i k a r a i s h i , D.M. (1983) Nucleic Acids Res. 11, 3317-3332. 1122
Vol. 160, No. 3, 1989
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
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