Expression System With Trans-Acting DNA Segments

1.Field of the Invention

This invention relates generally to gene expression systems comprising an expression vector and a "trans-acting DNA segment" where the expression vector comprises the gene or genes to be expressed and one or more cis-acting regulatory elements which are responsive to a trans-acting factor produced by said "trans-acting DNA segment". More specifically the invention relates to such gene expression systems where said "trans-acting DNA segment" and said cis-acting regulatory elements comprise one or more segments of the genome from a Bacillus species.

2. Description of the Background Art

Gene expression systems, where the expression of a specific gene is regulated in the transcriptional phase by the binding of a repressor molecule to the DNA sequence comprising the operator for the gene concerned, thus preventing RNA polymerase from binding to the promotor, and in which induction occurs through the binding of an inducer to the repressor molecule, which causes a conformational shift in the repressor, decreasing the affinity of the repressor for the operator, are well known in Eschericia coli.

Such operator-repressor control systems as for example the lac operon therefore have for a number of years been used for the expression of foreign genes in E. coli.

Recently an interest has been raised for the cloning and expression of foreign genes in bacilli, especially Bacillus subtilis, for a number of reasons. In contrast to E coli, B. subtilis is not a pathogen, and it does not produce endotoxins. Also it possesses a secretory system that releases proteins into the culture medium in large quantities. Its genetic map is well characterized, and a great deal of information on large-scale cultivation of B. subtilis is available since the organism is widely used in industry. One disadvantage of B. subtilis strains, the formation of spores, has been circumvented by the development of asporogenic B. subtilis strains.

The gene expression systems hitherto known in bacilli that work on the transcriptional level are, however, not regulated by induction, but use a different mechanism. Gene regulation in these organisms is controlled by .sigma.-factors, which are proteins that bind to the RNA polymerase and determine the recognition site for RNA initiation. Such systems cannot easily be used for the controlled expression of a foreign gene.

The attempts that have been made in expressing foreign genes in B. subtilis have until now concentrated on using .alpha.-amylase derived secretion vectors (Palva et al: Gene 22 (1983) 229-235; Ulmanen et al.: J. Bacteriol 162 (1985) 176-182; and Meyer and Fiechter: Appl. Environ. Microbiol. 50 (1985) 503-507).

One general problem with organisms that have cloned genes is the low expression of foreign or abnormal proteins. Gene expression depends on environmental conditions which determine cellular physiology. In many cases, optimal culture conditions for product formation are not identical with optimal growth conditions, and in some cases the foreign gene products may even be toxic to the host organism.

The results from the attempts to express foreign genes in bacilli mentioned above have indicated that either the regulation is performed on the translational level, or the foreign gene product is decomposed through the proteolytic action from exoenzymes native to B. subtilis. The yields of foreign proteins have therefore in these attempts been very variable.

In E. coli this problem has been alleviated by the use of inducible operator-repressor expression systems as those mentioned above.

Use of the lac repressor-operator from E. coli in B. subtilis has been reported by Yansura and Henner (Proc. Natl. Acad. Sci. U.S.A. 81 (1984) 439-443). This solution, however, suffers from the disadvantage that the lac operator-repressor system is not native to bacilli.

For a number of years it has been known that the production/occurrence of a number of enzymes in bacilli could be induced by xylose and other sugars in the growth medium, but the mechanism behind this phenomenon has remained unknown. The enzymes induced by xylose are those necessary for xylan utilization in bacilli such as described by I. G. Roncero, J. Bacteriol. 156 (1983) 257-263.

For a number of years it has also been known that this xylose induction only occurs when a suitable growth phase has been obtained by the culture, i.e., when the logarithmic growth phase has ceased and the culture has reached a certain maturity.

The structural gene for the production of xylanase has been cloned and used for the expression of xylanase in E. coli and B. subtilis (Japanese published patent No. 75286-A and 9198978-A).

It has now surprisingly been found that the mechanism behind the induction of the production of xylan digesting enzymes in B. subtilis is of the operator-repressor type.

Further it has been possible to isolate the genes involved and determine the structure and base sequence of said operator-repressor expression system in the genome of B. subtilis.

This suggests further that the production of other enzymes that is induced by the addition of other sugars, also is governed by such operator-repressor systems.

Consequently the invention provides for a novel gene expression system comprising an expression vector and a trans-acting DNA segment, the expression vector comprising the gene or genes to be expressed and one or more cis-acting regulatory elements which are responsive to a trans-acting factor produced by said "trans-acting DNA, segment" and wherein said "trans-acting DNA segments" and cis-acting regulatory elements are obtainable from the genome of a Bacillus species.

In a second aspect the invention provides for a method for stimulating the production of a gene product, which comprises:

a) inserting a "trans-acting DNA segment" into a host, said "trans-acting DNA segment" being obtainable from the genome of a Bacillus species, which segment codes for a trans-acting factor;

b) inserting an expression vector into said host, said expression vector comprising the gene or genes coding for the gene product or products to be expressed and one or more cis-acting regulatory elements which are responsive to said trans-acting factor produced from said "trans-acting DNA segment";

c) cultivating the host; and if necessary

d) at an appropriate time when the population of the host has reached a desirable level adding a compound that inactivates said trans-acting factor to the culture in order to derepress said cis-acting regulatory elements, and thereby initiate the production of said desired gene product or products.

In a third aspect the invention provides for a vector for use in expressing gene products, comprising DNA coding for the gene product or products and one or more cis-acting regulatory elements which respond to a trans-acting transcription factor which is coded for by a DNA segment obtainable from a Bacillus species, and which DNA segment may be included in the vector.

In a fourth aspect the invention provides for a vector for use in expressing gene products, comprising a DNA segment obtainable from a Bacillus species and coding for a trans-acting transcription factor which represses one or more cis-acting regulatory elements that are coupled to DNA coding for the gene product or products, and which DNA coding for the gene product or products and one or more cis-acting regulatory elements may be included in the vector.

In a fifth aspect the invention provides for novel microorganisms transformed with a vector according to the third or fourth aspect above.

In a sixth aspect the invention provides for the use of the novel gene expression system of the invention for the production of transformed microorganisms, and the use of such transformed microorganisms for the production of gene products heterologous to the original microorganism.

The invention will be explained in more detail in the following with reference to the drawings, wherein

FIG. 1 shows the restriction map of the xylose regulon comprising the gene expression system of the invention,

FIG. 2 shows the structure of a vector pSX 50 according to the invention,

FIG. 3 shows the structure of another plasmid pSX 56 according to the invention, and,

FIG. 4, 5, 6, and 7 show the structures of yet another four vectors according to the invention.

FIG. 8 shows the base sequence for the gene coding for the repressor xylR.

FIG. 9 shows the base sequence for the two promoter-operator sequences P.sub.1 O.sub.1 and P.sub.2 O.sub.2.

As indicated above the invention relates in its first aspect to a novel gene expression system comprising an expression vector and a transacting DNA segment, the expression vector comprising the gene or genes to be expressed and one or more cis-acting regulatory elements which are responsive to a trans-acting factor produced by said "trans-acting DNA, segment" and wherein said "trans-acting DNA segments" and cis-acting regulatory elements are obtainable from the genome of a Bacillus species.

One system originates from Bacillus subtilis and comprises in its native state two cis-acting regulatory elements (promotor-operators) each regulating the transcription of two genes, and one DNA segment coding for a trans-acting factor (repressor gene) to which the two promotor-operators are responsive.

The system regulates the production of the enzymes necessary for the growth on xylose and xylose-polymers of Bacillus subtilis, and the repressor molecule is derepressed by the presence of xylose in the medium.

Because of the growth phase regulation it is, however, not necessary to omit the inducer molecule (xylose) from the growth medium, since the induction only occurs after the logarithmic growth phase has ended, and an appropriate population has been reached.

This allows for the system to be self regulating when used to transform bacilli, and xylose is included in the initial growth medium.

In the elucidation of the system it was surprisingly found that the repressor gene was situated between the two regulated operons, and that the transcription was in the opposite direction of the transcription of the two operons.

For the use of the system for the purposes of the invention it is not necessary to employ all of the elements described above, but only the repressor gene in connection with at least one of the promotors.

One embodiment of the system of the invention thus contemplates a gene expression system, wherein the expression vector comprises one cis-acting regulatory element which is responsive to said trans-acting factor.

In bacilli the repressor gene is already present, and it is consequently not necessary to insert the repressor gene in a vector used to transform bacilli.

In another embodiment the invention allows for the simultaneous production of at least two different heterologous gene products by employing an expression vector comprising two different cis-acting regulatory elements both of which are responsive to said trans-acting factor.

Although it is not necessary it is contemplated that for the use of the system in microorganisms other than B. subtilis, the "trans-acting DNA segment" is situated in the expression vector.

Also it has been found that the results obtained by transforming bacilli are superior when using expression vectors containing the repressor gene, so that the organism actually has several genes coding for the repressor.

In a number of experiments it has been shown that even though the repressor gene in the native system is transcribed in a direction opposite to the transcription of the two operons, the repressor functions no matter what the direction of transcription is.

The system has been shown to be operative also in microorganisms of other genera such as in E. coli, except that in such cases a promotor native to the pertinent microorganism must be inserted in front of the bacillus operator.

As mentioned above the structure and base sequence of the gene expression system of the invention for B. subtilis that is inducible with xylose has been determined, and thereby it was found that the gene coding for the repressor, xylR, has the base sequence shown in FIG. 8. ##STR1## the two promoter-operator sequences, P.sub.1 O.sub.1 and P.sub.2 O.sub.2 are shown in FIG. 9. ##STR2##

The structure of the regulon responsible for the transcription in B. subtilis of the genes necessary for growth on xylose was elucidated as follows:

DNA from the Bacillus subtilis strain DN497 was digested partially with the restriction enzyme BglII and fragments from 2 to 10 kb were isolated from a 1% agarose gel. The DNA was then ligated with BamHI-cut, dephosphorylated plasmid pBR322 (from New England Biolabs), Beverly, Mass. and thereafter transformed into E. coli MC1000 r.sup.- m.sup.+. Selection was carried out on ampicillin plates and the transformants were sprayed with a 2 mM solution of 4-methyl-umbelleferyl-.beta.-D-xyloside (from Sigma) Chemical Co., St. Louis, Mo.

Colonies carrying the xynB gene coding for the enzyme 1,4-.beta.-D-xylosidase were detected as fluorescent when exposed to UV-light due to hydrolysis of the substrate.

The gene xynB was found on a 8.4 kb fragment, mapped more precisely, and sequenced. It was shown to be the last gene in a two-cistronic operon where the first gene (xynC) codes for a protein with long stretches of hydrophobic amino-acids.

In E. coli transcription of xynB was shown to originate partly from within xynC and partly from plasmid promoters. When cloned onto pDN1050 and transformed back into B. subtilis DN497 a strong transcription came from a 320 bp MspI-BglII fragment upstream of xynC.

DNA downstream of xynC was shown to repress this transcription but only in the absence of xylose. This indicated that a repressor gene (xylR) was present on the initial clone. SDS-page gel electrophoresis showed that the cloned DNA contained another gene that was regulated in the same way as xynB but transcribed from its own promoter. This was shown to be the gene coding for the enzyme xylose isomerase (xylA).

The xylR gene lies between xynB and xylA and is read from the other strand on the DNA (FIG. 1). The gene is 1152 bp long which means that the repressor monomer consists of 384 amino acids.

The two promoters controlled by the repressor were mapped by the enzyme Sl as described by Gilman and Chamberlain (1983), Cell, 35, 285-93.

The structure of the xylose regulon is shown on FIG. 1 which also contains a restriction map of the regulon, and wherein the direction of transcription is indicated with arrows.

In the following examples the promotor-operators P.sub.1 O.sub.1 and P.sub.2 O.sub.2, and the repressor gene xylR were used in the construction of a number of vectors used to transform various microorganisms in order to demonstrate the operativeness of the gene expression system of the invention. The examples are in no way to be construed as limiting the invention.

Also in the above text and in the examples below a number of microorganisms were used which are listed below:

Preparation of plasmids and chromosomal DNA and transformation of Bacillus subtilis and E. coli were conducted according to the following general procedures. Digestion with restriction enzymes, Bal 31 nuclease treatment, oligo-DNA-linker insertion and ligation with T4-ligase of DNA were performed with enzymes from New England Biolabs under the conditions suggested by the supplier.

All Bacillus subtilis strains were derivatives of Bacillus subtilis 168 (Spizizen, Proc. Natl. Acad. Sci., 44: 1072-78, 1958). RUB200: aroI906, amyE07, amyR2 was obtained from Dr. Frank Young, University of Rochester, New York. SL438:trpC2 (sporulation and protease deficient) was obtained from Dr. Kim Hardy, Biogen, Geneve. DN497: amyE07, amyR2 is an aro.sup.+ transformant of RUB200 with chromosomal DNA from SL438, QB1133: aroI906, metB5, sacA321, amyE was from Dr. Georges Rapoport, IRBM, Paris. QB1130:dal, metB5, sacA331, amyE was obtained from the Bacillus Genetic Stock Center, Columbus, Ohio. DN608: dal-1, metB, sacA, amyE was an aro.sup.+, dal-1 transformant of QB1133 with chromosomal DNA from QB1130.

SHa28: metB, sacA, amyE, xynB, was made by congression into DN608 with chromosomal DNA from DN497 and that has a 4 bp deletion in xynB (a disrupted PstI site). SHa165: A protease weak nitrosoguanidine mutant of DN497.

E. coli: MC1000: F.sup.- .DELTA.lacX74 galF, galK, .DELTA.(leu-ara)7697 (Casadaban, M. J., and Cohen, S. N. (1980), J. Mol. Biol. 7697, 138, 179-207). This strain was made r-m+ by conventional methods.

pBR322: Sutcliffe, J. G. (1979). Cold Spring Harbor Symp. Quant. Biol. 43, 77-90.

pDN 1050: Danish Patent Application No. 5940/84.

Competent Bacillus subtilis cells were prepared according to Yasbin et al. (J. Bacteriol. 121: 296-304, 1975). Cells were then harvested by centrifugation (7000 rpm, 3 min.), resuspended in one tenth volume of supernatant including 20% glycerol, frozen in liquid nitrogen and stored at -70.degree. C. For transformation, frozen cells were thawed at 42.degree. C. and mixed with one volume buffer (Spizizen's minimal medium (Spizizen, Proc. Natl. Acad. Sci. U.S.A. 44:1072-78, 1958)) with 0.4% glucose, 0.04M MgCl.sub.2 and 0.002M EDTA). DNA was added and the mixture incubated with shaking at 37.degree. C. for 20 min. Cells were then plated on appropriate selective media.

An overnight culture of E. coli K-12 strain No. 802 in LB (10 g Bacto tryptone, 5 g Bacto yeast extract and 10 g NaCl per liter water, pH 7.0) was diluted 100 fold in 500 ml LB and grown at 37.degree. C. to OD.sub.450 =0.4. The culture was chilled, left 15 min. on ice, spun for 15 min. at 3000 rpm (in a Sorvall GS3 rotor), resuspended in 200 ml cold 0.1M CaCl.sub.2, left on ice for 20 min., spun for 10 min. at 3000 rpm, resuspended in 5 ml cold 0.1M CaCl.sub.2 and left on ice for 20 hours. Cold glycerol was then added to 10% and aliquotes were frozen in liquid nitrogen and stored at -70.degree. C. Frozen cells were thawed on ice, DNA was added, the mixture incubated 45 min. on ice, 2 min. at 37.degree. C. and then plated on an appropriate selective medium.

E. coli were grown overnight in 250 ml LB, 0.4% glucose and an appropriate antibiotic. Cells were harvested by centrifugation and resuspended in 4 ml Buffer 1 (0.025M Tris.HCl, pH=8.0, 0.01M EDTA, 0.05M glucose, 2 mg/ml lysozyme). The suspension was incubated at 0.degree. C. for 15 min. and then mixed with 8 ml Buffer 2 (0.2M NaOH, 1% SDS). Then 6 ml Buffer 3 (3M NaAcetate, pH=4.8) was added, the mixture kept at 0.degree. C. for 60 min. followed by centrifugation for 20 min. at 19000 rpm (ca. 45000 g in Sorvall SS34 rotor). The supernatant was precipitated with 0.6 vol cold isopropanol and resuspended in 1.2 ml 5TE (0.05M Tris.HCl, pH=8.0, 0.005M EDTA), plus 20 .mu.l boiled RNase A (Boehringer) (2 mg/ml). 30 min. later the solution was layered on top of 4.0 ml Buffer 4 (80 g CsCl plus 56 ml 5TE) and 0.1 ml EtBr (10 mg/ml ethidium bromide) in a VTi65 tube. The mixture was centrifuged at 45000 rpm for 20 h. The plasmids were then removed from the tube, dialyzed and extracted as described in section VI.

Plasmids were prepared as described for E. coli strains (see section III) but with the following modifications. Growth was in LB including 0.01M potassium phosphate, pH=7.0 and an appropriate antibiotic (e.g. 6 .mu.g/ml chloramphenicol) and if required 100 .mu.g/ml D-alanine. After harvest, cells were incubated at 37.degree. C. with lysozyme. Buffer 2 was replaced by a mixture of one volume Buffer 2 and three volumes Buffer 5 (0.2M glycine, 0.2M NaCl and 1% SDS). The remaining steps were the same as in Section III.

Plasmids from 5 ml B. subtilis in LB (including 0.01M phosphate pH=7.0 and appropriate antibiotics and D-alanine if required) were prepared as in section IV except: 1: volumes of buffers were reduced four fold. 2: 0.5 ml phenol and 0.5 ml chloroform were added after Buffer 3. 3: After centrifugation at 19000 rpm, the supernatant was precipitated with ethanol, resuspended in 400 .mu.l Buffer 6 (0.05M Tris.HCl pH=8.0, 0.1M NaAcetate), the plasmids were again precipitated, resuspended in 400 .mu.l Buffer 6, precipitated, washed and resuspended in 100 .mu.l TE (0.01M Tris.HCl, pH=8.0, 0.001M EDTA) with 1 .mu.g/ml boiled RNase A (Boehringer).

A pellet of frozen cells from about 50 ml culture was resuspended in 1.1 ml Buffer (0.05M Tris.HCl, pH=7.4, 0.1M NaCl, 25% sucrose). 100 .mu.l lyzosyme (25 mg/ml) and 150 .mu.l EDTA (0.5M, pH=8.0) were added. The mixture was incubated at 37.degree. C. for 30 min. 2 ml 0.2% SDS were added followed by incubation for 30 min. at 37.degree. C. 1 g CsCl and 0.05 ml EtBr (10 mg/ml) were added per 0.95 ml mixture and the mixture was centrifuged at 45000 rpm, 15.degree. C., for 20 hours in a VTi65 rotor (Beckman).

The DNA was located under a long wave UV lamp and removed by puncturing the tube with a syringe. EtBr was extracted with isopropanol and the solution dialyzed for 2 hours against TEE (0.01M Tris.HCl, pH=8.0, 0.01M EDTA). The solution was then adjusted to 8 ml with TEE and extracted twice with phenol and once with chloroform. The DNA was precipitated with 0.1M NaCl and cold ethanol and dissolved in 1 ml TE (0.01M Tris.HCl, pH=8.0, 0.001M EDTA). The solution of chromosomal DNA was kept at 4.degree. C.

Two basic gene expression systems according to the invention were constructed into which different genes could be closed and expressed by either P.sub.1 O.sub.1 and P.sub.2 O.sub.2 under regulation from xylR.

In FIG. 2 a restriction map is shown of one of the basic vectors pSX 50 used in the following examples. As indicated in the figure it comprises the promotor-operator P.sub.1 O.sub.1 on a 322MspI to BglII (converted to ClaI) fragment, a B. pumilus xynB gene on a 2.5 kb ClaI to SalI fragment, and the B. subtilis xylR gene on a 1380 bp BamHI to SphI fragment from 134 bp before the xylR start to 82 bp after its stop. The vector was inserted into the plasmid pDN 1050 (2.5 kb).

FIG. 3 shows the corresponding restriction map of the other basic vector pSX 56. As indicated it comprises the B. subtilis xylR gene and the promotor-operator P.sub.2 O.sub.2 on a 1475 bp EcorI to ClaI fragment from 215 bp before the xylR start to 82 bp after its stop together with the same xynB gene as in pSX 50. This vector also was inserted into the plasmid pDN 1050 (2.65 kb).

B. subtilis SHa28 (xynB.sup.31) transformed with either of these two plasmids shows an increase by a factor of 150 to 200 in xylosidase activity as measured by the hydrolysis of p-nitro-phenyl-beta-D-xylopyranoside (Sigma), when grown on 0.2% xylose compared to growth without xylose.

The xynB ClaI-BamH fragment on pSX 50 was replaced by the apr gene from Bacillus licheniformis coding for the extracellular alkaline protease subtilisin Carlsberg to obtain the plasmid pSX55 (FIG. 4).

In supernatants of SHa28 transformed with this plasmid grown with and without xylose, no substilisin band was seen without xylose, whereas it was the predominant band when the cells were grown in the presence of 0.2% xylose.

The calf prochymosin gene was fused to the B. pumilus xynB gene resulting in a gene that codes for a fusion protein that consists of the first 12 amino acids from xylosidase followed by prochymosin.

This fusion gene was cloned into ClaI-HindIII on pSX 50 and pSX 56 to obtain the plasmids pSX 52 and pSX 59 (FIGS. 5 and 6).

These plasmids were used to transform B. subtilis SHa 165 (DN 497 (protease.sup.(-) (nitrosoguanidine))).

The Western blot of intracellular fluid showed that the prochymosin gene is under xylose control.

The E. coli rrnB terminator was cloned into pSX 52 behind the prochymosin gene to obtain the plasmid pSX 62 (FIG. 7) that was used to transform SHa 165. Western blot analysis showed that this increases the amount of prochymosin markedly (about 40% of total protein).

A deletion of 820 bp between the first and third EcoRV sites in the xylR gene in pSX 62 was performed to obtain a plasmid, pSX 71, wherein the xylR gene was destroyed. This plasmid was used to transform SHa 165.Western blot analysis clearly indicates that the production of prochymosin no longer is under xylose control.