Note : Les descriptions sont présentées dans la langue officielle dans laquelle elles ont été soumises.
~ 3 9
Field of Invention
~- The invention relates to the production of interferon (IFN). More
1 ~
specifically it relates to the production of large amounts of human
; interferons of the fibroblast (~) or leucocyte (~) types by suitable
bacteria, into which a fragment of human genomic DNA was introduced. Human
DNA taken directly from blood cells is cloned in a suitable ~-phage. High
interferon production can be obtained in bacteria infected by this recomb-
inant ~-phage and the interferon can be recovered and purified from the
bacter'ial lysates resulting from this infection. The genomic DNA is also
lo expressed in bacteria into which it has been introduced via a plasmid
expression vector.
BACKGROUND OF THE INYENTION
, . .
, - - Interferon, and especially human interferon is attaining an increasing
importance in a number of fields. Its production is rather cumbersome and
improvements in the processes of its production are of great importance and
value.
Expression of mammalian genes in bacteria such as E. coli is usually
prevented by the presence of intervening sequences interrupting the coding
sequence of the gene. There are, however, a certain number of genes that do
20 not have introns. Recently, Nagata et al. (1980)(Nature 287, 401-8) showed
that human leucocyte interferon-~ genes also lack introns. They could
detect low levels of expression of these genes in E coli.
Human diploid fibroblasts, induced by double-stranded RNA, contain at
least two mRNAs coding for interferon (Weissenbach et al.,l980, PNAS 77,
7152-7156). One mRNA, 0.9 kb long (llS) corresponds to the major interferon
species IFN-~l produced by these cells, whose amino acid sequence was
partially determined (Knight et al., 1980, Science 207, 325-6). Cloning via
cDNA of this IFN-~l mRNA, using E. coli plasmid pBR322 as vector, has been
achieved (Goeddel et al., 1980, Nucleic Acid Res., 8, 4057-4075). The
30 nucleotide sequence of these DNA clones corresponds to that determined for
the protein and, after construction of expression plasmids, the IFN-~l cDNA
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was shown to direct the synthesis of human interferon in E. coli. We have
isolated human genomic fragments carrying the IFN-~l gene (Mory et al., 1981
Eur. J. Biochem. 120, 197-202), and the IFN-ac gene. These genes lack
introns and can be, therefore directly expressed in E. coli.
Summary of the Invention
The invention relates to a process wherein a specific fragment of
human genomic DNA, extracted from human blood cells is cloned in a bacterio-
phage vector, and used directly to program the synthesis of IFN in bacteria,
which are cultivated resulting in the production of interferon. In this
13 method, there is,therefore, no need for the lengthy preparation and
cloning of full-length complementary DNA (cDNA) from mRNA. According to the
present invention, a suitable piece of DNA is taken directly from a readily
available human cell, such as white blood cell, and cloned in a ~-phage
vector. The required IFN gene is not interrupted by introns and is thus
-- capable to direct IFN synthesis in bacteria. High IFN activity was
produced by infecting suitable bacteria, such as E. coli by a recombinant
phage co~taining a human DNA insert with the IFN-~l gene or IFN-~C gene.
IFN was recovered and purified from bacterlal lysate resulting from such an
infection. Phages were found to be suitable vectors for introducing human
20 DNA fragments into bacteria; ~ Charon 4A phage was especially suitable, and
led to high IFN production. The invention further relates ~o the introduction
of such cloned human genomic DNA fragments into plasmid expression vectors,
which have been provided with strong promotors. The process can be carried
out with different IFN-~ as well as Ir,~-~l genes, provided that these lack
introns.
In one embodiment, DNA from a human adult was fragmented by partial
Eco RI digestion and cloned in ~ Charon 4A. The thus obtained clone,
. .
designated as Clone C15, with a human DNA insert of about 17 kb, was
identified as containlng a gene for the fibroblast interferon IFN-~l.
30 Restriction mapping showed that this gene located on a 1.8 kb Eco RI fragment,
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;s not h1te11~t~d by introns. This human genomic DNA fragment is able to direct the
synthesis of active human IFN-~, in E. coli and in other suitable bacteria. A high IFN
activity can be recovered from phage lysates. Under certain conditions an activity of the
order of 107 U/liter was recovered from phage lysates. The Iysates are advantageously
subjected to chromatography, preferably on Cibacron Blue Sepharose* or on similar columns,
and the thus obtained interferon has the same immunological properties and species specificity
as IFN produced from human fibroblasts. Similar results were obtained with IFN-ac, whose
gene was identified in clone 18-3 containing a 13 kb human genomic fragment.
In a furthrr e1nbodiment the human genomic DNA fragment containing the IFN-~3, or
IFNac gene were introduced into a plasmid such as plasmid pBR322 containing the recA
promoter of E. coli. Cultures of E. coli transformed by these recombinant plasmids produced
large amounts of IFN-~ or lFNa respectively when the recA promoter was induced by
nalidixic acid. The IFN-~, genomic fragment was then cut next to the codon for the first
methionine of the mature IFN-~I and ligated to the ribosomal binding site of the E. coli lac
promoter. This lac promoter was modified so as 1(~ contain the RNA polymerase binding site
of the tryptophan promoter. Witll this hybrid tr~ c promoter, the genomic IFN-~ DNA
was able to produce 108 U/liter IFN-~I in E. coli minicell strain P679-54. Similarly
satisfactory yields of IFNac wcrc obtained when tllc IFNac gene was appropriately linked to
the trp-lac promoter. In all cascs the IFN activity was recovered from the bacterial cell by
Iysis with Iysozyme and 30% prnpylelle glycol, and was then purified as for the phage Iysates
on a hydrophobic chromatograplly support. For IFN-~I a preferred support is Cibacron Blue
Sepharose. Elution can be effected by substances such as ethylene glycol or preferably
propylene glycol. Further purificaLion of IFN-~, or ac can be effected by immunoaffillity
chromatography on monoclonal antibody columns or by other conventional techniques.
It is, therefore, clear that human genomic DNA fragments can be used for high yield
production of human IFN in E. coli and other suitable host bacteria. As set out above, the
process according to the present invention
* Trade Mark
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1 comprises of introducing a fragment of human genomic DNA into a suitable
vector such as a phage, infecting d culture of bacteria with such phages
resulting in the lysis of such bacteria, and recovering the resulting
interferon content of the lysate. The invention, relates to the novel
phages obtained by the introduction of human genomic DNA and especially
to recombinant phages of the ~-type such as clone C15, resulting in
IFN-~2 and 18.3, resulting in IFN-~C. The invention further relates to
a process for the production of interferon by introducing human genomic
DNA into a suitable phage, recovering from said phage a suitable DNA
o section, introducing same into the expression of plasmid of suitable
bacteria, cultivating same and recovering the desired interferon. Other
and further objects of the invention will become apparent from the
following detailed description which is to be construed in a non-
limitative sense.
An important advantage of this invention is that genes from healthy
or diseased individuals can be compared for their ability to produce IFN,
thereby allowing us to study genetic defects in IfN production.
MATERIALS AND METHODS
Preparation of human gene library:
High molecular weight DNA was prepared from peripheral blood cells
of an adult with ~-thalassemia. DNA aliquots (40 ~9) were separately
digested 30 min with 100, 200 or 300 units Eco RI, then heated 10 min to
65~C and applied together on a 10-40% sucrose gradient as described. DNA
, fragments between 10 and 20 kb were ligated with T4 DNA ligase as
- ~ described by Mory et al. (1980, Mol. Biol. Reports 6, 203-208) to
Charon 4A DNA arms prepared by Eco RI digestion according to Maniatis et al.
(1978, Cell 15, 687-701).
, ~, r
1~
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1 In vitro packaging was done as described by Hohn and Murray (1977,
PNAS 74, 3259-3263) by mixing several 8 ~1 aliquots of the ligation
reaction (0.5 ~9 vector DNA and 0.125 ~g human DNA) with 50 ~1 extracts
of E. coli BHB2688 [N205 recA (~ imm 434 cIts b2 red 3 Eam4 Sam7)/~]
and BHB2690 [N205 recA (~ imm 434 cIts b2 red 3 Dam 15 Sam 7)/A].
Per ~g recombinant DNA, 3x105 pfu were obtained, compared to lo8 pfu/~g
intact ~ DNA. A total of 1.8xi06 recombinant phages were diluted in
6 ml 10 mM Tris-HCl pH 7.5, 10 mM MgS04, 0.01% gelatine. After adding
0.1 ml chloroform and removing debris by microfuge centrifugation, the
phages were amplified 105-fold by plating on E. coli DP50 (Leder et al.,
1977, Science 196, 175-177) at 4x103 pfu/15 cm plate. For screening,
2x104 pfu were seeded on 15 cm plates and duplicate nitrocellulose
filters lifted sequentially as set out by Benton et al., (1977, Science
196, 180-182). This work was done under P3 containment conditions.
Preparation of IFN-~l cDNA probe:
Poly A from human foreskin fibroblasts FSll cultures induced
4 hours by 100 ~g/ml poly(rI):(rC), 50 ~g/ml cycloheximide (with 2 ~g/ml
actinomycin D for the last hour) was prepared, and the two peaks of
interferon mRNA were fractionated by sucrose gradient centrifugation
as detailed, Weissenbach et al., (1980 PNAS 77, 7152-7156 ; ~eissenbach
et al., 1979, Eur.J.Biochem. 98 I-8). The llS mRNA (1.5 ~g) was used
to prepare RNA-cDNA hybrids with reverse transcriptase from avian
myeloblastosis virus (J. Beard) and oligo(dT) as before Weissenbach
et al., (1980 ,PNAS 77, 7152-7156). The RNA-cDNA hybrids were direct1y
cloned according to Zain et al., (1979, Cell 16, 851-861), but using
dCTP for tailing the hybrids and dG-tailed, Pst I-cleaved pBR322 as
vector (chang et al., 1978, Nature 275, 617-624). A total of
12,500 tetr ampS transformants of E. coli MM294 were obtained as oùtlined
by Stenlund et al.,(l980, Gene 10, 47-52). Colony hybridization
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1 was done with 32P-cDNA probes transcribed either from llS mRNA
(6 ~9) of induced FSll cells or from total poly A -RNA (3.7 ~9)
of non-induced cells. The cDNA synthesis was initiated with a
synthetic complementary primer,(see Narang et al., 1979,
Methods Enzymol. 68, 90-98), 5'GAGATCTTCAGTTTC 3', which includes
the ~ II site of the IFN-~l sequence. With 32p 5~ end labeled -
(Houghton et al., ~1980', Nucl.Ac. Res. 8, 1913-1931) primer, an
expected 640 nucleotides-long cDNA was observed only when induced
RNA was used as template. To prepare the probes, 20 pmoles primer
were annealed with each RNA in 4 ~1 0.4 M KCl at 30~C for 60 min,
then incubated in 25 ~1 with 200 ~Ci each of 32P-~-dATP and dCTP
(both 400 Ci/mmol), 0.5 mM each of dGTP and TTP, 50 mM Tris-HCl
pH 8.3, 4 mM MgC12, 5 mM dithiothreitol, 50 ~g/ml actinomycin D,
4 mM pyrophosphate and 30 units reverse transcriptase for 2 hrs
at 37~C. After adding 25 ~g E. coli DNA, the reaction was treated
by 0.3 N NaOH 60 min at 70~C, neutralized and filtered through
Sephadex G-50 in 50 mM Tris-HCl pH 8, 0.1 M NaCl, 10 mM EDTA,
0.5~~ dodecyl sulfate. From each RNA, Sx106 cpm cDNA was obtained.
Colonies grown on nitrocellulpse f11ters were fixed, and DNA
denatured as described by Thayer (1979 Anal. Biochem. 98, 60-63).
Each filter was prehybridized with 10 ml 6XSET (SET=150 mM NaCl,
2 mM EDTA, 30 mM Tris-HCl pH 8) lOxDenhardt's solution (Denhardt
1966, Biochem.Biophys.Res.Comm. 23, 641-646), 0.1% Na pyrophos-
phate, 0.1% dodecylsulfate, 50 ~g/ml denatured E. coli DNA for
4 hrs at 67~C. Filters were hybridized at 67~C for 14-18 hrs in
the same solution with o.SxlO6 cpm/filter of either of the two
32P-cDNA probes, 10 ~g/ml poly A and 2.5 ~g/ml poly C. Filters
were washed for 1 hr at 67~C in prehybridization solution, then
3 times more for 30 min at 67~C with 3XSET, 0.1% pyrophosphate,
0.1% dodecylsulfate, then 60 min at 25~C with 4XSET, see Maniatis
(1978, Cell 15, 687-701). Filters were dried and exposed to
Agfa Curix X-ray films with intensifying screens for 1-2 days at -70~C.
~! 3 9 8 2 9
Out of 3,500 colonies screened, 14 hybridized preferentially
to primered cDNA from induced mRNA, while 130 hybridized also to
primered cDNA of non-induced mRNA. DNA (0.3 ~9) of plasmids from
the first group was hybridized on filters (Kafatos et al., 1979,
Nucl. Ac. Res. 7l,1541-1552) with the 5'-end 32P-labeled primer
itself (0.3 pmoles, 4X106 cpm) in 6XSSC, lOxDenhardt's solution
at 35~C for 21 h, followed by washing with 6XSSC (900 mM NaCl,
, 90 mM Na citrate) at 35~C. One clone I-6-5 was strongly positive
and DNA sequencing (see Maxam et al., 1980, Methods Enzymol. 65,
~0 499-560) showed that it contained about 370 nucleotides from the
- 3'-side of the IFN-~l sequence. There were screened another 50,000
clones prepared as previously by introducing dC-tailed ds-cDNA from
sucrose gradient purified induced mRNA in the Pst I site of pBR322:
the proportion of IFN-~l clones were found to be 0.16% (80 clones)
as compared to 0.65% IFN-~2 clones.
The çlone IFN-~l I-Ç-5 des~r,ibed above and prepared from FS-ll
mRNA was used to screen the human library.
Isolation of ~he genomic clone:. IFN nl clone 15
Plasmid DNA from IFN-~l cDNA clones was labeled by nick-
translation, according to Rigby et al., (1977, J.Mol. Biol. 113,
237-251) to 2X108 cpm/~g DNA and hybridized at lo6 cpm/filter to
the human gene library. Preparation of filters, DNA denaturation
and hybridization procedures were as described above. Phages from
plaques giving positive hybridization, were replated at a density
of 1-2x102 pfu on 9 cm plates and rescreened. This procedure was
repeated 3 times until more than 95% of the plaques on the plate
hybridized to IFN-~l cDNA. Phage clone C15 was isolated from one
such plaque.
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Phages were grown in liquid cultures as described by Blattner
et al., (1977, Science 196, 161-169). E. coli DP50 were grown
overnight in 1% tryptone, 0.5% NaCl, 0.5~ yeast extract, 0.2%
maltose, 0.25% MgS04, 0.01% diaminopimelic acid, 0.004% thymidine.
About 0.3 ml of the culture was mixed for preadsorbtion with 0.3 ml
of 10 mM MgS04, 10 mM CaC12 and 107 phages for 20 min at 37~C. The
cultures were then diluted into a 2 liter flask with 500 ml of
prewarmed medium containing 1% NZ amine, 0.5% yeast extract, 0.5%
NaCl, 0.1% casamino acids, 0.25% MgS04, 0.01% diaminopimelic acid,
.. .. .
lo 0.004% thymidine, and incubated with good aeration for 15-18 hrs
at 37~C. After lysis was complete, the cell debris were removed
by centrifugation in the cold 15 min at 7,000 rpm in a Sorvall GSA
rotor. From this clarified lysate the phages were precipitated
with 7% polyethylene glycol 6000 and purified by two successive
CsCl gradients. Phage C15 DNA was phenol-purified and its structure
analyzed by restriction enzyme digestions, horizontal agarose gel
electrophoresis in 20 mM tris base, 10 mM Na acetate, 1 mM EDTA
with 0.5 ~g/ml ethidium bromide, transferred to nitrocellulose
filters (Southern ,1975, J. Mol. Biol. 98, 503-517) and hybridi-
_ - 20 zation to nick-translated IFN-~l cDNA as above. Eco RI fragments
of C15 DNA were subcloned in the Eco RI site of pBR322 for precise
restriction mapping of the plasmid DNA according to the established
- procedure, see Bolivar (1979, Methods Enzymol. 68 245-267).
Assay of interferon activity in phage lysates:
Clarified phage IFN-~l C15 lysates, prepared as above were
dialyzed against phosphate buffered saline (PB5) for 7 hrs. A
10 ml aliquot was loaded on a 0.3 ml column of Cibacron Blue-
Sepharose CL6B (Pharmacia Fine Chem.). The column was washed with
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1 10-15 ml of 1 M NaCl, 0.02 M Na Phosphate buffer pH 7.2, and
then with 10 ml of 50% propylene glycol in the wash solution.
. Fractions (0.5 ml) were collected and stored at 4~C; in some
cases 0.1% human serum albumin was added for stabilization.
Interferon activity was assayed, as described by Weissenbach
et al., (1979, Eur. J. Biochem. 98, 1-8) by diluting each
fraction serially in a 95-well microplate. Each well received
2-3x104 FSll human fibroblasts in 0.1 ml Minimum Essential Medium
(Gibco), 5% fetal calf serum (FCS), 0.5% Gentamycin. After
18 hrs at 37~C, medium was removed and vesicular stomatitis virus
(VSV) was added at 1 pfu/cell in medium with 2% FCS. Inhibition
of the cytopathic effect was recorded 30 to 40 hrs after infection,
in comparison to IFN-~ NIH standard G023-902-527. The antiviral
activity was also measured by the reduction of 3H-uridine incorpora-
tion after VSV infection as described previously (Weissenbach et al.,
1979,l Eur. J. Biochem. 98,'1-8). Anti-serum to IFN-~ was obtained
from rabbits and assayed as before (Weissenbach et al., 1979, Eur.
J. Biochem. 98, 1-8). For the neutra~ization test, 0.1 ml anti-
serum (titering 104 U/ml) or non-immune serum was mixed with 0.2 ml
20 of a 50% suspension of protein A-Sepharose beads (Pharmacia Fine
Chem.) in PBS, for 1 h at 37~C. The beads were washed twice with
PgS and 0.1 -ml of bacterial interferon (100 U/ml) were added. After
-~ 2 hrs at 37~C, the beads were centrifuged and the supernatants
assayed for inhibition of 3H-uridine incorporation in VSV infected
cells.
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1 Isolation of genomlc clone: IFN-ac c10ne 18-3
Two short single-stranded oligonucleotides, chemically synthesized
as above, were used to screen directly the human gene library. The
oligonucleotides are complimentary to common sequency of IFN-a genes
and had the sequence 5'CTCTGACAACCTCCC 3' and 5'CCTTCTGGAACTG 3'. The
oligonucleotides were used after 5' labeling, as above, either directly or as
primers for cDNA synthesis on R~A from Sendai-virus induced human leukemic
cells. The 32P-oligonucleotides or primed cDNAs were hybridized to a
total of 500,000 ~'recombinant phages, as demonstrated above. Approximately
o 5x105 cpm were used per 9 cm nitrocellulose filter. Hybridizations were
done in plastic sealed cooking pouches in minimal volumes of liquid.
Hybridization with the 15 base primers were performed as follows: First,
prehybridization in 6xSSC, 10 x Denhardts at 37~C for 4 hrs; then,
hybridization in 6xSSC, 10 x Denhardts at 31~C for 18 hrs, and washes,
3-4 times, 30 min each in 6xSSC at 37~C or until no more counts were
found in wash. For hybridization with the 13 base primer, hybridization
and washing temperatures were dropped to 30~C. A total of 16 phages gave
positive hybridization and were further analyzed by restriction mapping
and DNA sequencing. Clone 18-3 was demonstrated to carry 3 IFN-~ genes,
20 one of which has the sequence identical to the cDNA clone ~c ~f
Goeddel et al., (1981, Nature 290, 20-25). Clone 18-3 was purified as
described for clone C15 above. Expression of clone 18-3 in ~ bacterio-
phage and after insertion into expression plasmid vector is described in
the Results.
~ -- 10 --
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r~ 3 9 ~ 2 9
The invention will be further described in the following by way of example only and
with reference to the attached drawings wherein:
Figure lA shows the schematic structure of IFN-~I clone C15 DNA
(a): Schematic map of ~ Charon 4A. The two arms are shown in full line. (b): Structure of
the human DNA insert in clone C15, the blackened area shows the Eco RI fragment which
hybridizes to IFN-~, cDNA. (c): Enlargement of the blackened fragment from b, is shown
as a double line. The single line is part of ~ right arm. PL is the ~ leftward promoter. (d):
Position of the IFN-~3, mRNA. The upper scales is for (a) and (b). The lower scale for (c)
and (d). For details see text,
Figure lB illustrates the schematic structure of IFN-oc clone 18-3
The restriction map of the inserts of two ~ Charon 4A clones is shown. The IFN-ac gene is
desi~n~ted by the arrow alpha-c*. Two other IFN-a genes are present near IFN-c~c. The
inserts shows the Eco RI 2 kb fragment 18-33 which contains the IFN-ac genes and was
recloned n the recA plasmid, as explained in the text. Symbols for restriction enzyme site are
shown;
Figure 2 shows the results of an assay of interferon produced by genomic clone
IFN-~3, C15 on Blue-Sepharose
Crude Iysate of E. coli DP50 infected by phage C15 was fractionated as described in Methods
and Materials and IFN-activity was assayed in each fraction (~). Protein concentration
was measured in the same fractions (-------). A parallel chromatography and assay of Iysate
from ~ Charon 4A phage is shown (Cl [1 );
Figure 3 illustrates the results of a titration of genomic clone IFN-~, C15 interferon.
A fraction of phage C15 IFN from the column in Figure 2 (about 103 U/ml), was diluted 1:40
and then serially diluted in the microplate for assay of IFN by dilution of VSV RNA synthesis
(o o). Standard human fibroblast interferon 25 U/ml was assayed in parallel (-------).
Control without VSV (C~) and with VSV without IFN (--) are shown. The two columns at
tlle right show the .esldual activity of the phage C15 IFN (at final dilution 1:40) after
adsorption on immobilized anti IFN-~ or non-immune IgG, as described in Methods; and
- 11 -
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Figure 4 illustrates the growth and IFN production in E. coli containing plasmid TL11.
The TL11 plasmid contains a hybrid trp-lac promoter and the coding sequence for mature
human IFN-~l, ori~inSlting from the human genomic fragment as described in the text.
Bacterial cultures were grown in a 1 liter New Brunswick fermenter and at the indicated
times, bacteria were lysed by lysozyme-propylene glycol and IFN activity assayed on human
cells challenged with VSV. The IFN activity is calculated per ml of bacterial culture.
RESULTS
1. Structure of ~enomic IFN~, C15 clone:
This phage clone was isolated from a library of human DNA which had been partially
digested with Eco RI and cloned in the arms of ~ Charon 4A. The clone hybridized strongly
to two different IFN-,BI cDNA probes, independently prepared from mRNA fractions of two
strains of human fibroblasts. Digestion of the phage DNA by Eco RI showed, in addition to
the two ~ a~ms, four fragments of 12, 2.6, 1.84 and 0.6 kilobases (Fig. lA). Transfer to
nitrocellulose by the method of Southern (1975, J. Mol. Biol. 98, 503-517), and hybridization
with nick-translated DNA from the IFN-~, gene. This Eco RI fragment was recloned in the
Eco RI site of pBR322; Restriction analysis of this 1.84 kb subclone with B~1 II, Pvu II,
Pst I, Hinc Il and ~q I, and hybridization with partial and full-length IFN-~I cDNA probes,
allowed to conclude that the coding sequence for IFN-,~I preprotein (Hinc II site) starts about
350 nucleotides from the Eco RI site (Fig. lA). The distances between the various restriction
sites in the genomic DNA are the same as in the cDNA sequence within experimental error
(Table 1). No unexpected restriction sites were found within the IFN-~3, coding region,
indicating the absence of any sizeable intervening sequence.
Partial Eco RI digests of C15 DNA showed that the 0.6 kb Eco RI fragment is located
between the 1.84 and 2.6 kb Eco RI fragments. A Bam HI site was found in the 2.6 kb, but
not in the other Eco RI fragments of the human DNA insert. The 1.84 kb Eco RI fragment,
that hybridizes to IFN-~, cDNA, was found on ~ 9.6 kb Bam HI fragment
- lla-
~ Ir. ~
~ rir, .
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of C15 DNA. As shown in Figure 1, this fragment can originate
only from the Bam HI site of the ~ right arm (5.1 kb from Eco RI),
leaving 4.5 kb for the Eco RI-Bam HI segment of the human insert,
and indicating that the 1.84 kb Eco RI fragment must be located
,ext to ~ right arm. The gene orientation (Fig. l~ was determined
as follows. When C15 DNA was cut with Pvu II and hybridized to
the full-length or to the 3'-half of IFN-~l cDNA, a 0.66 kb fragment
hybridizing only to the 5'-end of IFN-~l was found. But, when
the 1.84 kb Eco RI piece was cut with Pvu II, the 5'-end of IFN-~1
was on a smaller 0.54 kb fragment. Since no Pvu II site was found
in the 0.6 kb Eco RI piece of the human insert, the 0.66 kb Pvu II
fragment must end in the ~ right arm and, hence, the 5'-end of
IFN-~l is closest to the A right arm. The structure shown in Fig. lA
is supported by several other restriction mapping experiments using
Hind III, Sma I and ~ II digestions. The coding sequence of the
IFN-~1 gene in clone C15 was, therefore, inserted about 1,775
nucleotides away from the strong ~ PL promotor that controls left-
ward transcription (Williams et al., 1980 , Genetic Engineering
j Vol II, pp201-281, Plenum Corp.), and in the proper leftward orient-
: 20 ation. This together with the absence of detectable introns,
prompted us to investigate if interferon could be produced in
E. coli infected by the C15 recombinant phage.
. 2. Recovery of interferon biological activity from lysates of
E. coli infected by the IFN-~l C15 phage:
Phages from clone C15 were grown in 500 ml cultures of E. coli
-- DP50 as described in Methods. Ten ml of the clarified lysate was
~' dialyzed and loaded onto a small Cibacron Blue-Sepharose column (0.3 ml)
:~
and the fractions were assayed for the inhibition of Vesicular
Stomatitis virus (VSV) cytopathic effect, with an IFN-~ standard
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as reference. In one exper;ment, where the phage titer in the
lysate was 1.3x101~ phages/ml, the interferon activity pattern
shown in Fig. 2 was observed. A total of 7,500 units of IFN
activity were recovered in the fractions eluted by 50% propylene
"
~- glycol - 1 M NaCl from the column. This would correspond to
0./5x106 units/liter lysate. In the crude lysate, however, the
measurable activity was much lower suggesting that some material
in the lysate prevented correct assay of IFN activity. In a
reconstruction experiment, standard human IFN-~ was added to a
wild type ~ Charon 4A lysate and indeed the activity measured
was only one tenth of the input. When this mixture was passed
on the Blue-Sepharose column, 75% of the input activity was
recovered. In a control run, lysate from wild type ~ Charon 4A
phages (without adding IFN was analyzed, and no IFN activity
was found (Fig. 2).
The chromatographic behavior of IFN from lysates of clone C15
may be variable. In an experiment where the phage titer was
3xlOll pfu/ml, the IFN activity was high but was not retained on
the Blue-Sepharose column. In this experiment, the total
20 activity recovered from the column amounted to 70-80,000 units
IFN for an input of 10 ml lysate (7-8xlO6 units/liter). The
effluent fractions were readsorbed on a second Blue-Sepharose
column: this time the activity was retained on the column, but
again eluted by washing the column just with PBS. Human IFN-~l
- should normally be eluted from Blue-Sepharose only by hydrophobic
solvents (Knight et al., 1980, Science 207, 525-526). Therefore,
standard human IFN-~ was mixed with the same phage lysate and
applied to the column: 30% of the activity was not retained and
recovery of activity was only 25%. This suggests that components
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1 of this lysate probably destabilized the interaction of IFN-~, in
particular that produced by the bacteria, with Blue-Sepharose.
Even though interferon was not retained on the column, over 90%
of the protein of the lysate were removed from the active fractions
which had a specific activity of 4-5x105 U/mg protein. This
partial purification was essential to remove the chemicals that
~ masked the ac~ivity in the crude lysates. In one experiment,
~~ clone C15 IFN activity was also recovered after chromatography of
the lysate on carboxymethyl-Sepharose (not shown).
o 3 Properties of interferon produced in E. coli infected by
clone C15
The interferon activity recovered after the chromatographic
step, reduced 3H-uridine incorporation in VSV-infected human cells,
treated by actinomycin D (Weissenbach, 1979, Eur.J.Biochem. 98, 1-8).
The titration curve obtained for the bacterial IFN-~ was similar to
that for standard human IFN-~ (Fig. 3). To test the immunological
properties of the bacterial IFN, the partially purified product
was mixed with rabbit anti IFN-~ serum (inactive on IFN-~) or with
rabbit non-immune serum which had been prebound to protein A-
. 20 Sepharose. After centrifugation, the supernatant was assayed for
IFN activity: anti IFN-~ serum removed all the interferon activity,
while the activity remained when non-immune serum was used (Fig. 3).
The bacterial IFN (20 U/ml) was similarly neutralized when just
mixed with anti IFN-~ (20 U/ml) on the cell culture, and assayed
- by inhibition of VSV cytopathic effect.
The species-specificity of the bacterial interferon was
assayed by comparison of various cell types. As human IFN-~, the
product of clone C15-infected E. coli, showed less than 10% activity
on monkey kidney cell BSC-l and Bov;ne MDBK cells as compared to
30 human cells. There was no detectable anviral activity on mouse L
or A9 cells (Table 2). The same results were obtained with
6,000 U/ml of the bacterial IFN produced by clone C15.
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The present invention demonstrates, therefore, that the IFN-~l
gene, isolated directly from partial Eco RI frag~ents of human genomic
DNA by cloning in ~ Charon 4A, can be expressed and leads to the
accumulation of significant amounts of ~FN activity in the culture
lysates. The activity produced is clearly fibroblast interferon (~)
as shown by its immunological properties and its species-specificity.
The activity is produced by the bacterial culture only in response to
;nfection by the IFN-~l C15 phage clone. The IFN activity produced
by clone 15 in E. coli, resembles human IFN-~ in its chromatographic
o properties on Cibacron Blue Sepharose. The chromatographic step is
essential to recover hish activity (up to 7X106 U/liter) from the
bacterial lysate. Interferons provide therefore the first examples
of biologically active proteins that are produced by bacteria under
the direction of a piece of human DNA taken directly from the genome
of one individual.
4. Genomic IFN-~C 18-3 clone
This clone was identified by direct hybridization of short,
oligonucleotides, synthesized chemically to be complementary to sequences
in IFN-~. From a total of 0.5x106 genom;c, 16 clones were positive in
20 hybridization. The Eco Rl fragments hybridizing to the oligonucleotides
were sequenced and clone 18-3 was shown as in Fig. lB, to contain a
2 kb Eco RI fragment 18-33 (insert of Fig. lB) in which the gene for
IFN-~C is located. This gene is, clearly, the source of the mRNA which
gave rise to the IFN-aC clone reported by Goeddel et al., (1981, Nature
290, 20-25). Clone 5-1 represents an overlapping DNA fragment. Together,
clone 5-1 and clone 18-3 carries,in addition to IFN-~C, two other IFN-a
genes designated a-c2 and a~c4 (Fig- 1~).
""-'- 3!1 ~
~1 t
133982~
.
5. Expression of human IFN genomic fragment under recA promotor control
The recA promotor is considered to be one of the strongest E. coli
promotors. Normally, it is tightly repressed by the product of the lex
gene, eYen when present on a multicopy plasmid such as pBR322. It is
induced, in the presence of damaged DNA, to cleave its own repressor
and undergoes induction to very high levels (Sancar and Rupp, 1979~
PNAS 76, 3144-3148), The standard inducers for recA are nalidixic acid
. (whi.ch blccks DNA synthesis) or mitomycin C (which cross-links DNA).A plasmid, pDR1453, containlng the cloned recA gene was used to
isolate the promotor on a ~I-BamHI fragment of about 1 kilobase. This
was ligated into pBR322 that had been opened up with ClaI and BamI to
construct plasmid RAP-l. The TaqI-ClaI ligation restores the ClaI site
in this case, al10wing the plasmid to be uniquely opened in the third
codon of the recA gene. RAP-2 was constructed by cutting RAP-l with
Eco RI and ClaI, filling in the st;cky ends and religating which restores
the RI site. When RAP-2 is opened at the RI site, foreign DNA can be
inserted at the 3rd codon of the recA protein.
The RAP-l vector was used for indirect expression of interferon
activity by genomic fragments from the human genomic library. The
20 IFN-~l gene and several isolated IFN-~ genes of the ~c subclass, produced
strong interferon activity (as determined by the standard antiviral assay)
when inserted into this plasmid. The RI fragments of DNA on which these
genes reside (Fig. lA and B) were subcloned into the RI site of the RAP-l
plasmid. The plasmid was placed in a recA host, the bacteria grown
and induced with nalidixic acid, the cells harvested, lysed by lysozyme
plus 30% propylene glycol and the extract assayed for antiviral activity.
The level of activity is clearly dependent upon induction by nalidixic
acid, the optimum being at 50 llg/ml (Table 3). Interestingly, in some
cases, the genomic fragment produces activity in both possible orientati~ns
30 relative to the recA promotor. The IFN-~l and IFN-~ genes which ShQ~
activity were all located on DNA Eco RI fragments of 1.8-2 kilobases,
so that the distance from the promotor to the ATG start codon of the
--~6--
~ =
~ ~ ~ ~
. .
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interferon gene is on the order of hundreds of nucleotides.
These experiments prove that the promotor is functioning as
expected, and, they allow quick determinations of which interferon-
like genes from the gene library can be active.
6. High expression of IFN-~l gene under the control of tryp-lac
hybrid promotor
The plasmid PLJ3 (Johnsrud, PNAS, 1978, 75, 5314-5318) contains
two lac p~omotors each 95 base pair long separated by 95 non-related
nucleotides. This 285 nucleotides fragment is inserted in the Eco RI
site of the plasmid PMB9. The 95 base pair long lac sequences contain
the operator and promotor sequence and stops just before the ATG of the
~-galactosidase. A coding DNA sequence with an ATG initiator, inserted
at the proper distance from the ribosomal binding site of the ~-galacto-
sidase gene, should be correctly expressed in E. coli cells. The 285
base pairs Eco RI fragment was recloned into pBR322 at the Eco RI site;
the recombinants were screened by growing the cells on plates containing
40 ~g/ml X-gal and 15 ~g/ml tetracycline. Only positive blue colonies
were pooled and the DNA purified by CsCl gradient centrifugation.
Two orientations of the lac promotors are expected; towards the
20 ampicillin gene or towards the tetracycline gene of pBR322. Since we
are interested in having only the Eco RI site, located between the lac
ribosomal binding site and the pBR322 sequence, this site was protected
by binding RNA polymerase to the plasmid DNA, while the distal site was
open by Eco RI restriction, filled in with the Klenow fragment of DNA
polymerase and religated. After transformation of MM29~ E. coli cells,
plasmids were isolated and the distance between the Eco RI site and the
Bam HI site of pBR322 was measured. The plasmids containing a 375 base
pair fragment were those in which the lac promotors are toward the
- tetracycline gene, while those containing a 670 base pair fragment
(375+295 b.p.) had the lac promotors towards the ampicillin gene.
1~
13 39829
1 From the Eco RI 1.84 kb subclone of the IFN-~l genomic fragmentwe cut a HincII-~II fragment containing the preinterferon sequence.
r~~ The mature IFN-~l protein contains at its NH2-terminal end, a
methionine which can be used as an initiator codon in E. coli. There
are two AluI sites close to this ATG codon separated by 13 nucleotides,
one AluI site is 8 nucleotides in front of the ATG, while the other is
2 nucleotides after the ATG. A partial AluI digestion was performed
on the HincII-~II fragment and fragments around 510 base pairs were
isolated from agarose gels. The vector containing the lac promotors
lo towards the tetracycline gene was restricted with Eco RI, the site
filled-in by DNA polymerase and re-cut with BamHI. Upon ligation of
the AluI~ II fragments to the filled-in Eco RI-BamHI vector, the
Ecc RI site is restored. To be able to differentiate between the
.
-- clones containing the ATG codon (13 nucleotides longer) the clones
obtained were restricted with Eco RI and Pstl; the clones containing
the expected 151 base pairs fragments were sequenced. The Eco RI site
- was then reopened and the distance between the ribosomal binding site
and ATG shortened by Bal 31 digestion, and religation. E. coli cells
transformed by these plasmids were screened for IFN-~l production.
One clone, L-ll, was found to produce about 3xlC6 U/liter of IFN-~.
The lac promotor region in this clone was cut with ~e_HI, i.e. 17 nucleo-
tides before the start of the mRNA. To cut out the IFN-~l gene, the
enzyme Sau3a was used which cuts the DNA just 3 nucleotides beyond the
termination codon of IFN-~l. This HpaII-Sau3a lac-IFN-~l fragment was
introduced between the ClaI and HindIII sites of a tryp promotor plasmid
prepared as follows. A 180 nucleotide long ~ I fragment from
-21 to -201 before the start of the tryp mRNA, was cut out from the tryp
plasmid pEP121-221, and cloned in the ClaI site of pBR322. We selected
the orientation in which the tryp promotor fragment is oriented clock-
wise. This operation restores a ClaI site at position -21 of the t~
promotor. After ligation to the lac-IFN-~l fragment a hybrid promotor
1~
:~
1~39829
1 tryp-lac is formed before the IFN-~l gene. This plasmid TL-ll, was
used to transform E. coli MM294 or E. coli minicell strain p679-54.
These bacteria produce lo8 U/liter of IFN-~I under fermentor culture
to an OD650 of 10, demonstrating that the ~FN-~l genomic DNA fragment
is very active (Fig. 4).
.- ~
",
Iq
t . ~ ."~~: '
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1 TABLE 1: Restriction sites in IFN-~l cDNA and gene
DISTANCES BETWEEN SITES
Restriction Calculated from Measured from
**
*
sites ~1 cDNA sequence ~1 genomic DNA
nucleotides nucleotides
I-Pvu II 255 250
Hinc II-Pvu II 204 210
- Hinc II~ II 570 570
Pvu II -~ II 366 360
o Pst I -Bgl II 363 360
* From Taniguchi et al., 1980 Gene 10 (11-15).
** Measured from 1.84 kb Eco RI fragment.
The Hinc II and ~ I site taken into consideration are those
closest to 5'-end of gene.
TABLE 2: Species-specificity of bacterial interferon produced
by genomic IFN-~l C15 clone
INTERFERON TITER, U/ml
Interferon Source Human Monkey Bovine Mouse Mouse
FSll BSC-l MDBK L A9
cells cells cells cells cells
1. Human FSll cells 1,500 32 32 < 4 < 4
2. E. coli infected by C15 clone 1,000 32 32 < 4 < 4
The bacterial IFN was used after chromatography of the C15 lysate
on Cibacron Blue-Sepharose as in Fig. 2.
- 20 -
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TABLE 3: IFN-~ and ~ activities produced by genomic fragments in the
recA-plasmid M P-l
IFN activity
- Exp. Clone Conditions U/ml
1. RAP-l (1833)-IFN-~C + nalidixic acid 500
RAP-l (1833)-IFN- c ~ nalidixic acid < 32
2. RAP-l (1833)-IFN-~C right orientation 1000
RAP-l ( 631)-IFN-~1 right orientation 3000
RAP-l ( 631)-IFN-~1 opposite orientation750
Clone RAP-l ~1833) contains the Eco RI fragment with IFN-~C gene (Fig.lB).
o Clone R~P-l ( 631) contains the Eco RI fragment with IFN-~I gene (Fig.lA).
Fragments are inserted at the beginning of the recA gene. Orientation is
given with respect to recA promotor orientation.
