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Cloning & Characterization of Plasmid Replication: F'lac & R6-5 Plasmids Study, Summaries of Biotechnology

The isolation and characterization of replication regions of the E. coli plasmids R6-5 and F'lac using an EcoRI-generated fragment of a Staphylococcus aureus plasmid as a selection vehicle. The study demonstrates the proximity of plasmid replication origins, replication genes, and incompatibility determinants.

What you will learn

  • How were the replication regions of R6-5 and F'lac isolated and characterized?
  • What are the replication regions of the E. coli plasmids R6-5 and F'lac?

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Proc.
Nat.
Acad.
Sci.
USA
Vol.
72,
No.
6,
pp.
2242-2246,
June
1975
Cloning,
Isolation,
and
Characterization
of
Replication
Regions
of
Complex
Plasmid
Genomes
(DNA/restriction
endonuclease/incompatibility/R-plasmids/heteroduplex
analysis)
KENNETH
TIMMIS,
FELIPE
CABELLO,
AND
STANLEY
N.
COHEN
Department
of
Medicine,
Stanford
University
School
of
Medicine,
Stanford,
California
94305
Communicated
by
Allan
Campbell,
April
4,
1975
ABSTRACT
EcoRI
endonuclease-generated
DNA
frag-
ments
carrying
replication
regions
of
the
F'lac
and
R6-5
plasmids
have
been
cloned
and
isolated,
using
as
a
selec-
tion
vehicle
a
nonreplicating
ampicillin-resistance
DNA
fragment
derived
from
a
Staphylococcus
aureus
plasmid.
Heteroduplex
analysis
of
the
constructed
plasmid
chimeras
and
the
parent
replicons
has
localized
the
cloned
R6-5
replication
region
to
a
DNA
segment
between
kilobase
pair
coordinates
1.0
and
88.0
on
the
R6-5
map.
Physical
proximity
between
the
plasmid
replication
functions
and
the
locus
governing
plasmid
incompatibility
has
been
shown
for
both
parent
replicons.
The
cloning
method
reported
appears
to
be
generally
applicable
for
the
identi-
fication
and
isolation
of
replication
regions
of a
variety
of
complex
genomes.
Rapid
progress
has
taken
place
recently
in
the
study
of
DNA
synthesis
involving
small
replicons
such
as
simian
virus
40
(1),
the
bacteriophages
M13
and
4X174
(1,
2),
and
the
colicin
El
plasmid
(Col
El)
of
Escherichia
coli
(3,
4).
In
contrast,
bio-
chemical
investigations
of
the
replication
of
large
replicons
such
as
the
E.
coli
chromosome,
the
sex
plasmid
F,
and
some
antibiotic
resistance
(R)
plasmids
have
been
hindered
by
the
genetic
complexity
and
structural
fragility
of
these
DNA
molecules.
The
recent
demonstration
that
recombinant
plas-
mids
are
capable
of
containing
and
utilizing
at
least
two
dis-
tinct
sets
of
replication
functions
(5)
has
made
evident
still
other
potential
difficulties
in
investigating
the
replication
of
large
genomes.
In
this
report,
we
describe
the
isolation
and
characteriza-
tion
of
replication
regions
of
the
E.
coli
plasmids
R6-5
and
F'lac
using
an
EcoRI-generated
fragment
of
a
Staphylococcus
aureus
plasmid
as
a
selection
vehicle.
The
staphylococcal
plasmid
DNA
fragment,
which
carries
genetic
information
for
penicillin-ampicillin
(Ap)
resistance,
and
which
apparently
lacks
an
origin
of
replication
in
its
original
host
(R.
P.
Novick,
personal
communication),
is
capable
of
propagation
in
E.
coli
only
when
linked to
another
EcoRI
DNA
fragment
carrying
functions
required
for
replication
in
this
bacterial
host
(ref.
6
and
A.
C.
Y.
Chang
and
S.
N.
Cohen,
unpublished
data).
Genetic
and
molecular
investigations
of
the
cloned
E.
coli
plasmid
replication
region
fragments
demonstrate
a
physical
proximity
between
plasmid
replication
origins,
replication
genes,
and
incompatibility
determinants.
MATERIALS
AND
METHODS
Escherichia
coli
K-12
strain
C600
(7)
and
nalidixic-acid
re-
sistant
(nalr)
mutants
of strains
CRT46
(8)
and
CR34
(9)
have
been
described.
Plasmid
R6-5
(10)
expresses
resistance
to
chloramphenicol
(Cm),
kanamycin
(Km),
streptomycin
(Sm),
and
sulfonamide
(Su).
The
pSC102
plasmid
was
con-
structed
by
in
vivo
ligation
of
EcoRI-treated
R6-5
DNA,
con-
sists
of
three
EcoRI-generated
fragments
of
R6-5,
and
ex-
presses
Km
and
Su
resistance
(11).
Plasmid
pSC101
codes
for
resistance
to
tetracycline
(Tc)
(9).
Plasmid
pSC113
was
constructed
in
vitro
(6)
and
contains
the
entire
pSC101
plas-
mid
plus
two
EcoRI-endonuclease-generated
fragments
of
the
S.
aureus
penicillinase
plasmid
pI258
(12);
it
codes
for
resistance
to
penicillin-ampicillin
and
Tc.
Plasmids
R100-1
and
R192-F7
(refs.
13
and
14,
kindly
provided
by
K.
Hardy)
are
derepressed
fertility
mutants
of
R100
and
R192,
and
ex-
press
resistance
to
Tc,
Cm,
Sm,
and
Su.
F'lac
is
the
classic
Paris
F'
plasmid
and
was
obtained
in
strain
DF109
(=
bromo-
deoxyuridine-resistant
isolate
of
DF87,
ref.
15)
from
D.
Frei-
felder
via
R.
P.
Silver.
The
procedures
used
for
conjugal
transfer
(16)
and
trans-
formation
of
plasmid
DNA
(17),
radioactive
labeling
and
iso-
lation
of
plasmids
(18),
sucrose
and
CsCl
gradient
centrifuga-
tion
(5),
construction
of
hybrid
plasmid
DNA
molecules
by
means
of
the
EcoRI
restriction
endonuclease
(11),
and
agarose
gel
electrophoresis
(5)
have
been
described.
Plasmid
hetero-
duplex
analysis
procedures
have
been
described
by
Sharp
et
al.
(19).
The
EcoRI
restriction
endonuclease
was
purified
from
E.
coli
strain
RY-13
according
to
Greene
et
al.
(20)
through
the
phosphocellulose
chromatography
step.
E.
coli
DNA
ligase
was
generously
provided
by
S.
Panasenko,
P.
Modrich,
and
I.
R.
Lehman.
RESULTS
Isolation
of
the
Selection
Vehicle.
Chang
and
Cohen
re-
cently
described
the
in
vitro
construction
of
a
Tc
and
Ap
resistance
plasmid
chimera,
pSC1
13,
that
contains
the
entire
pSC101
plasmid
replicon
plus
two
EcoRI-generated
frag-
ments
of
the
penicillin-ampicillin
resistance
staphylococcal
plasmid
pI258
(6).
Cleavage
of
the
pSC113
plasmid
chimera
with
the
EcoRI
endonuclease,
ligation
of
the
resulting
frag-
ments,
and
transformation
of
E.
coli
with
the
ligated
mixture
yielded
another
plasmid
(pSC122)
that
also
expressed
resis-
tance
to
both
Tc
and
Ap,
but
which
contained
only
one
of
the
two
EcoRI-generated
fragments
of
Staphylococcus
plasmid
DNA
originally
present
in
pSC113
(Fig.
1A).
This
Ap
frag-
ment,
which
is
the
larger
of
the
two
staphylococcal
EcoRI
fragments
contained
in
pSC113,
has
a
buoyant
density
in
CsCl
of
1.692
g/cm3
(Table
1).
Because
of
the
substantial
difference
in
the
buoyant
density
of
the
Ap
fragment
and
the
buoyant
density
of
the
pSC101
plasmid
(p
=
1.710
g/cm3)
the
two
DNA
species
can
be
separated
easily
by
preparative
cen-
trifugation
of
EcoRI-cleaved
pSC122
plasmid
DNA
in
CsCl
gradients
(Fig.
1B).
2242
Abbreviations:
Ap,
ampicillin-penicillin;
Cm,
chloramphenicol;
Km,
kanamycin;
Sm,
streptomycin;
Su,
sulfonamide;
Tc,
tetra-
cycline;
CCC,
covalently
closed
circular;
kb,
kilobase;
M.W.,
molecular
weight.
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Download Cloning & Characterization of Plasmid Replication: F'lac & R6-5 Plasmids Study and more Summaries Biotechnology in PDF only on Docsity!

Proc. Nat. Acad. Sci. USA Vol. 72, No. 6, pp. 2242-2246, June 1975

Cloning, Isolation, and Characterization of Replication Regions of Complex

Plasmid Genomes

(DNA/restriction endonuclease/incompatibility/R-plasmids/heteroduplex analysis)

KENNETH TIMMIS, FELIPE CABELLO, AND STANLEY N. COHEN

Department of Medicine, Stanford University School of Medicine, Stanford, California 94305

Communicated by Allan Campbell, April 4, 1975

ABSTRACT EcoRI^ endonuclease-generated^ DNA frag- ments carrying replication regions of the F'lac and R6- plasmids have been cloned and isolated, using as a selec- tion vehicle a nonreplicating ampicillin-resistance DNA fragment derived from a Staphylococcus aureus plasmid. Heteroduplex analysis of the constructed plasmid chimeras and the parent replicons has localized the cloned R6- replication region to a DNA segment between kilobase pair coordinates 1.0 and 88.0 on the R6-5 map. Physical proximity between the plasmid replication functions^ and the locus governing plasmid^ incompatibility^ has^ been shown for both parent replicons. The cloning^ method reported appears to be^ generally^ applicable^ for^ the identi- fication and isolation of replication regions^ of a^ variety^ of complex genomes.

Rapid progress has taken place recently in^ the study^ of DNA

synthesis involving small replicons^ such as^ simian virus^ 40 (1),

the bacteriophages M13 and 4X174 (1, 2), and the colicin El

plasmid (Col El) of Escherichia coli (3, 4). In contrast, bio-

chemical investigations^ of^ the^ replication^ of large^ replicons

such as the E. coli chromosome, the sex plasmid F, and some

antibiotic resistance (R) plasmids have been hindered by the

genetic complexity and structural fragility of these DNA

molecules. The recent demonstration that recombinant plas-

mids are capable of containing and utilizing at least two dis-

tinct sets of replication functions (5) has made evident still

other potential difficulties in investigating the replication of

large genomes.

In this report, we describe the isolation and^ characteriza-

tion of replication regions of the E.^ coli plasmids R6-5^ and

F'lac using an EcoRI-generated fragment of^ a^ Staphylococcus

aureus plasmid as a^ selection vehicle.^ The^ staphylococcal

plasmid DNA fragment, which^ carries^ genetic information^ for

penicillin-ampicillin (Ap)^ resistance,^ and^ which^ apparently

lacks an origin of replication in its original host (R. P. Novick,

personal communication), is^ capable^ of^ propagation^ in^ E. coli

only when linked^ to^ another^ EcoRI DNA^ fragment^ carrying

functions required for replication in this bacterial host (ref.

6 and A. C. Y. Chang and S. N. Cohen, unpublished data).

Genetic and molecular investigations of the cloned E.^ coli

plasmid replication region fragments demonstrate a^ physical

proximity between plasmid replication origins, replication

genes, and^ incompatibility determinants.

MATERIALS AND^ METHODS

Escherichia coli K-12 strain C600 (7) and nalidixic-acid^ re-

sistant (nalr) mutants of strains^ CRT46 (8)^ and^ CR34^ (9)

have been described. Plasmid R6-5 (10) expresses^ resistance

to chloramphenicol (Cm), kanamycin (Km), streptomycin

(Sm), and sulfonamide (Su). The pSC102 plasmid was con-

structed by in vivo ligation of EcoRI-treated R6-5 DNA, con-

sists of three EcoRI-generated fragments^ of^ R6-5, and^ ex-

presses Km^ and Su^ resistance (11). Plasmid pSC101 codes^ for resistance to^ tetracycline^ (Tc)^ (9).^ Plasmid^ pSC113^ was

constructed in vitro^ (6)^ and^ contains^ the^ entire^ pSC101^ plas-

mid plus two EcoRI-endonuclease-generated fragments of

the S. aureus penicillinase plasmid pI258 (12); it codes for

resistance to penicillin-ampicillin and Tc. Plasmids R100-

and R192-F7 (refs. 13 and 14, kindly provided by K. Hardy)

are derepressed fertility mutants of R100 and R192, and ex-

press resistance to Tc, Cm, Sm, and Su. F'lac is^ the classic

Paris F' plasmid and was obtained in strain DF109 (= bromo-

deoxyuridine-resistant isolate of DF87, ref.^ 15) from^ D.^ Frei-

felder via R. P. Silver.

The procedures used for^ conjugal transfer^ (16)^ and^ trans-

formation of plasmid DNA^ (17),^ radioactive^ labeling^ and^ iso-

lation of plasmids (18), sucrose and CsCl gradient centrifuga-

tion (5), construction of hybrid plasmid DNA molecules by

means of the EcoRI restriction endonuclease (11), and agarose

gel electrophoresis (5) have been described. Plasmid hetero-

duplex analysis procedures have been described by Sharp et^ al.

(19). The EcoRI restriction endonuclease was^ purified from

E. coli strain RY-13 according to Greene et^ al.^ (20) through

the phosphocellulose chromatography step. E. coli DNA^ ligase

was generously provided by S.^ Panasenko, P.^ Modrich,^ and

I. R. Lehman.

RESULTS

Isolation of the Selection Vehicle. Chang and^ Cohen^ re-

cently described the in vitro construction^ of^ a^ Tc^ and^ Ap

resistance plasmid chimera, pSC1 13, that^ contains^ the^ entire

pSC101 plasmid replicon plus two EcoRI-generated frag-

ments of the penicillin-ampicillin resistance^ staphylococcal

plasmid pI258 (6). Cleavage^ of^ the^ pSC113^ plasmid^ chimera

with the EcoRI endonuclease, ligation of the resulting frag-

ments, and transformation of E. coli with the^ ligated mixture

yielded another plasmid (pSC122) that^ also^ expressed resis-

tance to both Tc and Ap, but which^ contained^ only one^ of^ the

two EcoRI-generated fragments of^ Staphylococcus plasmid

DNA originally present in pSC113 (Fig. 1A). This^ Ap frag-

ment, which^ is^ the^ larger^ of^ the^ two^ staphylococcal^ EcoRI

fragments contained in pSC113, has^ a^ buoyant density in^ CsCl

of 1.692 g/cm3 (Table 1). Because of^ the^ substantial^ difference

in the buoyant density of the^ Ap fragment and^ the^ buoyant

density of the pSC101 plasmid (p =^ 1.710^ g/cm3) the^ two

DNA species can be separated easily by preparative cen-

trifugation of EcoRI-cleaved^ pSC122 plasmid DNA^ in^ CsCl

gradients (Fig. 1B).

Abbreviations: Ap, ampicillin-penicillin; Cm, chloramphenicol; Km, kanamycin; Sm, streptomycin; Su, sulfonamide; Tc,^ tetra- cycline; CCC, covalently closed circular; kb, kilobase; M.W., molecular weight.

Cloning of^ Replication Regions 2243

31

z

0-

0 10 20 FRACTION NUMBER

30

wC

CX

0 z m z CD) -i

co

FIG. 1. Isolation of staphylococcal (^) Ap-resistance DNA. (A) Construction of (^) pSC122 plasmid. One (^) microgram of (^) pSC DNA in (^50) ,u of a solution of 20 mM Tris.HCl pH 8.0, 1 mM Na2EDTA, 10 mM^ MgCl2 was^ digested^ for^30 min^ with^1 uA^ of EcoRI endonuclease prepared as previously described (5). The nuclease was then inactivated by incubation for 5 min at 600 and the DNA mixture (^) was ligated by addition of (^) (NH4)2SO4 (to 10 mM), NAD^ (to 100 uAM), bovine^ serum^ albumin (to 100 ug/ml), and 5 units of DNA (^) ligase. After (^) incubation at 140 overnight the mixture was used to transform cells (^) of E. coli K12 (^) C600. Cova- lently closed circular (CCC) plasmid DNAs prepared from transformant clones that (^) expressed Ap-resistance were (^) analyzed by electrophoresis of their EcoRI digestion products through an 0.8% agarose gel in Tris-borate buffer (5). One Ap-resistance plasmid, designation pSC122, contained only one of the two original staphylococcal EcoRI endonuclease cleavage products of the parent pSC113 plasmid. Fig. 1A is a photograph of an ethidium bromide-stained agarose gel containing the following EcoRI endonuclease-cleaved plasmids: 1, pSC101; 2, pSC113; 3, pSC122; and^ 4, Ap DNA^ fragment isolated as described in 1B below. (B) Isolation of Ap fragment DNA by buoyant density cen-

trifugation. Thirty-three micrograms of [3H]thymidine-labeled

pSC122 CCC-DNA^ (specific activity =^ 2.5^ X 103 cpm/pg) were cleaved with EcoRI (^) enzyme as described (^) above, dialyzed 4 hr against a solution of 10 mM Tris HCl, pH 8.0, 1 mM EDTA (TE buffer) to remove NP40 detergent present in the enzyme preparation, and then mixed with TE buffer to give a final volume of 8 ml. Solid CsCl was added (refractive index =^ 1.3985) and the solution (^) was centrifuged in a (^) bovine serum (^) albumin-coated centrifuge tube in a 50 Ti rotor at 36,000 rpm for 60^ hr^ at 200. Fractions were collected from a hole pierced in the bottom of the tube and the (^) radioactivity (0) in an (^) aliquot of (^) each fraction was measured (^) and the refractive index (^) was determined. Fractions indicated by the shaded area were pooled and dialyzed ex- haustively against TE buffer. This material was analyzed by agarose gel electrophoresis (Fig. 1A). About 10 jg of^ Ap fragment DNA was recovered.

Isolation of Replication Regions of the R6-5 and F'lac Plas- mids. Aliquots (1.5,ug) of Ap fragment DNA purified from the

FIG. 2. Analysis of R6-5-Ap and F'lac-Ap hybrid plasmids by agarose gel electrophoresis. CCC^ plasmid DNA^ preparations were cleaved to completion with EcoRI endonuclease and sub- jected to electrophoresis through 0.8% agarose slab gels as indicated in Fig. 1. Fragments of all plasmids are numbered from top to bottom in the gels, as was described previously (11). (A) 1, R6-5 + pSC135; 2, pSC135; 3, R6-5; 4, PSC136; 5, Ap fragment; 6, pSC139; 7, pSC102; 8, R6-5 + pSC102. (B) 1, pSC138; 2, pSC137; 3, F'lac; 4, pSC140; 5, Ap fragment; 6, pSC141. The^ pSC140 and pSC141 plasmids contain one or^ more other (^) fragments of F'lac in (^) addition to the replication region fragments.

pSC122 plasmid were separately mixed with equal amounts of

EcoRI-cleaved R6-5 or F'lac plasmid DNA and ligation and

transformation were carried out as described in Materials and

Methods and Fig. 1. Covalently closed circular (CCC) plas-

mid DNA samples isolated from 10 separate Ap-resistant

clones obtained by transformation with the R6-5 ligation

mixture were treated with EcoRI endonuclease and examined

by agarose gel electrophoresis; several representative plas-

mids are shown in Fig. 2A. All plasmid DNA preparations

had in common a single EcoRI fragment of the R6-5 plasmid

in addition to the Ap fragment; one of the clones (pSC136)

contained a second R6-5 DNA fragment (fragment XI, ref.

11) which was not essential for replication of the chimera.

Because fragments II and III of R6-5 have almost identical

mobilities in agarose gels, electrophoresis of a mixture of

EcoRI-cleaved pSC135 and R6-5 DNA (Fig. 2A-1) was car-

ried out to identify the R6-5 DNA fragment that enables

replication of the Ap fragment in E. coli. Mobility measure-

ments, using the other R6-5 bands present in gel 1 of Fig. 2A

as internal standards, identified the band having increased

fluorescence intensity as EcoRI fragment II of R6-5. A^ similar

co-electrophoresis experiment indicated that R6-5 fragment

II, and not the slightly smaller fragment III as was previously

believed (11), is contained also in the pSC102 plasmid (Fig.

2A-8). Parallel experiments indicated that a single EcoRI

fragment of F'lac (fragment VI of the parent plasmid) was

common to all of the F'lac-Ap plasmid chimeras isolated (Fig.

2B); several of the chimeras contained various other F'lac

Proc. Nat. Acad. Sci. USA (^72) (1975)

Cloning of^ Replication Regions 2245

63.9 kb from the ends of EcoRI fragment II in the complete

R6-5 plasmid and is situated 1.7 kb and 7 kb from the ends

of this fragment in pSC102. Thus, formation of the pSC

plasmid necessarily occurred by intracellular ligation of

separate DNA fragments, and not simply by in vivo recir-

culation of a single DNA segment containing the three EcoRI

fragments. Direct examination of the pSC102/R6-5 hetero-

duplex (data not shown) confirmed this interpretation.

The only region of homology seen in fifteen pSC135/pSC

heteroduplexes (e.g., Fig. 3D) is the 6.4 kb Ap fragment,

indicating that the EcoRI replication region fragments of

R6-5 and F'lac^ contain dissimilar base^ sequences. This is

consistent with the observed differences in replication-associ-

ated properties shown by F'lac and R6-5 (copy number,

acridine orange sensitivity, compatibility; Table 1 and ref.

22). The F'lac/pSC138 heteroduplex (Fig. 3E) shows a region

of homology 7.8 kb in length, which corresponds to the size

estimated by gel electrophoresis for the EcoRI replication

region fragment cloned from the F'lac plasmid (M.W.

5 X 106).

Compatibility Studies. Although incompatibility between

bacterial plasmids has been considered to be a property of

plasmid replication (23), direct evidence for a structural

interrelationship between these separate functions is lacking.

Using constructed Ap resistance plasmid chimeras containing

the replication regions of R6-5 or F'lac, we have investigated

compatibility of the plasmid chimeras with those plasmids

from which their replication functions have been derived

(Table 2). Incompatibility was studied by transformation

of the R6-5-Ap plasmid chimera pSC135, or the F'lac-Ap

plasmid chimera pSC138 into bacteria containing the parent

or a plasmid related to it, and was measured by the frequency

of expression of genes carried by the incoming plasmid in the

presence or in the absence of selection for determinants car- ried by the resident plasmid.

The pSC122 plasmid, which provided the Ap fragment for

these plasmid chimeras, is seen to be compatible with F'lac,

R6-5, R100-1, R192-F7, and pSC102 plasmids, and hence the

Ap fragment does not contribute to incompatibility. In con-

trast, the R6-5-Ap plasmid pSC135 is incompatible with

pSC102, R6-5, and other large plasmids (R100-1, R192-F7)

(Table 2) of the same incompatibility group as R6-5 (FII, ref.

22, and N. Datta, personal communication). The lowest incom-

patibility ratios (about 40) were observed between pSC135 (or

pSC102) and the R6-5, R100-1, and R192-F7 plasmids, which

appear to contain more than one set of replication functions (11, 24, 25). The greatest incompatibility ratio (about 800)

was observed between pSC135 and pSC102. The pSC

plasmid, which contains a replication region from F'lac, is

entirely compatible with plasmid R6-5 and its derivative

pSC102, consistent with the absence of nucleotide sequence

homology in the replication regions of the R6-5-Ap and F'lac-

Ap chimeras (Fig. 3D). As expected, pSC138 is incompatible

with the F'lac plasmid.

Measurements of incompatibility, which used a standard

conjugation method (16) and which employed nonconjugative

plasmids as resident replicons, yielded data which supported

the interpretations derived from Table 2. In the absence of

continued selection for antibiotic resistance determinants

carried by both plasmids, rapid segregation occurred in in-

stances where a high incompatibility index was observed.

However, in both transformation and conjugation experi-

ments, detectable segregation of or recombination between

('Sl1b REP^ jIR1^ (ISl)a^ IIR2{Sl)b 2.2^ I= 1.3 1.0^ I^ /MEE 88.0^ 55.0//\ 44.1 28.0 27.2^ I 2.2 1. 0/98.5 24.1 21. __ RTF - (^) r-DETERMINANT

FIG. 3. Heteroduplex analysis of R6-5-Ap and F'lac-Ap

hybrid plasmids. Standard procedures for plasmid DNA hetero- duplex analysis and electron microscopy were followed (19).

OX174 single-stranded^ and^ PM2^ duplex^ DNA^ were^ used^ as

internal standards for molecular length measurements (19, 27). The bar in each part of the figure represents 1 kb. Arrows indicate the junctions of single-strand (SS) and double-stranded (D) regions of the heteroduplexes. (A) Heteroduplex between^ pSC and R6-5^ plasmids. The^ region of homology is 11.5 kb in length and is^ located between^ 1.0^ and^ 88.0^ kb^ on^ the standard^ R6- physical map [shown in (B); see refs. 28 and 29]. A large single- stranded substitution loop (SS2) containing the two inverted repeats IR1 and IR2 represents the R6-5 segment absent in the pSC135 plasmid. The smaller substitution loop (SS1) represents the (^) Ap-DNA fragment contribution to pSC135. (B) Map of R6-5 showing the location of the cloned replication region. (C) The pSC135/pSC102 heteroduplex. The nonhomologous regions

comprising the Ap-DNA fragment (SS3) and the segment of

pSC102 (SS4) containing IR2 are indicated. (D) pSC135/pSC heteroduplex. The duplex region represents the Ap DNA frag- ment common to both plasmids. The replication region frag- ments of^ R6-5 (SS5) and F/lac(SS6) are indicated. (E) pSC138/ F'lac (^) heteroduplex. The region of homology is (^) 7.8 kb, which corresponds to^ the^ length of^ EcoRI^ fragment VI^ of^ F'lac.^ The single-strand substitution^ loops SS7^ and^ SS8^ are^ Ap DNA fragments and the nonhomologous segment of F'lac, respec- tively.

plasmids, as^ determined by examination of^ CCC-DNA, did

not occur in cells carrying compatible plasmid replicons.

DISCUSSION

The Ap-resistance EcoRI staphylococcal plasmid DNA frag-

ment used in these experiments has particular advantages

as a probe and vehicle for selection and cloning of replication

regions in E. coli. Because its buoyant density is substan-

tially different from the buoyant density of pSC101 DNA, the

fragment can be prepared in large quantities by CsCl den-

sity gradient equilibrium centrifugation of the EcoRI-cleaved

composite plasmid pSC122. The fragment can be separated

Proc. Nat. Acad. Sci. USA (^72) (1975)

2246 Biochemistry: Timmis et al.

from cloned E. coli plasmid replication region fragments by the same procedure, thus permitting the isolation of large amounts of replication region DNA for physical character- ization and in vitro studies. While the level of ampicillin resistance expressed by the staphylococcal DNA fragment in

E. coli (minimum inhibitory concentration, 200 ,g/ml) is

substantially lower than the (^) levels achieved by common

penicillin-ampicillin resistance plasmids indigenous to and

widely distributed among E. coli (Cabello and Cohen, in

preparation), it is sufficient for the selection of replication re-

gions as described here. Although earlier results, and those

presented in Table 2, suggest that at least two separate

replication regions are located on R6-5 and related plasmids

(11, 24, 25), all of the plasmid chimeras cloned in these studies

by the use of the Ap fragment selection vehicle contain a

unique EcoRI fragment. This finding suggests that essential

components of other R6-5 replication region(s) may be dis-

tributed on separate EcoRI fragments of the R6-5 plasmid.

The use^ of^ other restriction endonucleases for cloning replica-

tion regions of R6-5 should permit investigation of this pos-

sibility.

The demonstration that a 5.2 megadalton fragment of F'lac

DNA and a 7.6 megadalton fragment of the R6-5 plasmid

carry all of the functions required for replication of a DNA

fragment in E. coli indicates that the replication origin and

the replication genes of the F'lac and R6-5 plasmids are clus-

tered together in a small region of the genomes of these plas-

mids; similar clustering of replication origin and replication

genes has been observed in the genome of the bacteriophage X

The ability to clone specific segments of complex genomes

that carry genetic information for particular biological func-

tions such as DNA replication appears to be highly useful for

genetic and biochemical^ investigations of such functions.

The current experiments report the selective cloning and

study of^ EcoRI-generated replication region fragments of

two large plasmid genomes, R6-5 and F'lac. The methods

described are (^) potentially applicable for the isolation of DNA segments containing the (^) replication origin and/or genes of

any complex replicon capable of^ functioning in^ bacteria^ and

may be useful in the study of chromosome replication. The sequestration of replication functions onto small plasmid DNA molecules should facilitate in vivo and in vitro investiga- tions of gene products involved in replication. With appro- priate modification, the^ procedure describe1^ may also^ permit the isolation of^ particular DNA^ segments specifying functions involved in the (^) conjugal transfer of (^) plasmids.

These studies were supported by National Institute of Allergy

and Infectious Diseases Grant Al^ 08619, National^ Science

Foundation Grant GB-30581, and American Cancer^ Society

Grant VC-139. K.T. is the^ recipient of^ a^ postdoctoral fellowship

from the Helen Hay Whitney Foundation. We thank J. Zabielski

for technical assistance during part of this investigation.

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