NZ228441A

NZ228441A - Psg5 plasmid used in isolating is elements, transposons and mutated genes

Info

Publication number: NZ228441A
Application number: NZ228441A
Authority: NZ
Inventors: Gunter Muth; Alfred Puhler; Wolfgang Wohlleben; Bernhard Nussbaumer
Original assignee: Hoechst Ag
Priority date: 1988-03-23
Filing date: 1989-03-21
Publication date: 1991-06-25
Also published as: IL89687A0; NZ228442A; PT90091B; DE58905656D1; DK145989D0; DE3809691A1; ATE94904T1; AU3158389A; EP0334283A2; FI891334L; KR890014752A; JPH029369A; NO891266L; FI891334A0; EP0334283B1; DK145989A; HUT50510A; EP0334283A3; AU611004B2; PT90091A

Abstract

DNA segments from mutants can be obtained very straightforwardly by isolating from the strain to be mutated the total DNA, cleaving the latter into small fragments and integrating into a temperature- sensitive plasmid with another selection marker which is selectable in E. coli, transforming the hybrid plasmid population obtained in this way into the starting strain, selecting the transformants by selection for the marker, eliminating the hybrid plasmids by raising the temperature above the threshold of the temperature-sensitive plasmid, and selecting the mutants by renewed selection for the marker. Construction of a cosmid gene bank with the DNA of these mutants results, by selection for the marker which has been introduced and is selectable in E. coli and for the cosmid-intrinsic marker, directly in cosmids which contain the mutated gene.

Description

<div class="application article clearfix" id="description"> New Zealand Paient Spedficaiion for Paient Number £28441 22 8 4 4 1 NO DRAWINGS Priority Date(s): Complete Specification Filed: . Claw: .ft .&9 Publication Date: P.O. Journal. No: NEW ZEALAND Patents Act 1953 COMPLETE SPECIFICATION N. Z. t U2 1 MAR 1989 w/ ^ / o THE USE OF pSG5 AS A TEMPERATURE-SENSITIVE PLASMID We, HOECHST AKTIENGESELLSCHAFT, a corporation organized under the laws of the Federal Republic of Germany of D-6230 Frankfurt am Main 80/ Federal Republic of Germany, do hereby declare the invention, for which we pray that a patent may be granted to us, and the method by which it is to be performed, to be particularly described in and by the following statement:- - 1 - (Followed by 1A) -1ft- IIOBGIICT AKCDIENGBCBIiLCGIIAFT IIOD QO/r 0C0 22 8 4 4 1 Dg i IQJ/L'h Description The use of pSG5 as a temperature-sensitive plasmid European Patent (EP-B) No. 0/158,872 discloses the Streptomycetes plasmid pSG5 which can be isolated from a culture of Streptomyces ghanaensis DSM 2932. This plasmid is suitable for the preparation of hybrid vectors, for example for what are called shuttle vectors, which can, because of an incorporated E. coli replicon/ be multiplied in E. coli strains. Vectors of this type are disclosed, for example, in the European Patent Application with the publication No. (EP-A) 158,201. It has now been found that pSG5 is temperature-sensitive. The property of temperature-sensitivity for pSG5 is surprising because as yet no natural Streptomycetes plasmids having this property have been disclosed. Since pSG5 and the hybrid plasmids prepared with its replicon exhibit a wide host range, the new use of this plasmid according to the invention provides those skilled in the art with a large number of possibilities: When a plasmid which has the replicon of pSG5, containing a marker, is constructed and used to transform a compatible host strain, and then the temperature is raised above the threshold, the only transformants obtained after selection for the marker are those which have the plasmid integrated, in whole or in part, into the genome. Since such integrations essentially take place only in homologous regions of the genome, this method is suitable for finding such homologous regions in the genome of the host strain. EP-A 0,243,856 discloses a method for the preparation of mutants, which comprises isolating from the starting - 2 - 22 8 4 4 1 strain the complete DNA, converting it into short fragments, integrating these into a plasmid which contains a marker, is temperature-sensitive and replicates in the starting strain, and transforming the resulting hybrid population into the starting strain, selecting the transformants by selection for the marker, eliminating the hybrid plasmids by increasing the temperature above the threshold of the temperature-sensitive plasmid, and selecting the mutants by renewed selection for the marker. The term "short" fragments denotes DNA sections which are obtained with restriction enzymes which cut many times, such as Sau3A or Taal. but also with mechanical methods (ultrasound, shearing) and which contain neither the promoter region nor the translation stop signals. Because the only cells surviving after elimination of the plasmids in a selection for the marker are those which have taken up the plasmid DNA into their chromosome (which preferably takes place via the homologous DNA integrated in the plasmid), the mutants are obtained directly. The plasmid pSG5 is mentioned in EP-A 0,243,856 as a suitable starting plasmid. However, it is now possible according to the invention to dispense with mutation to give temperature-sensitive replication mutants when this plasmid is used. This means that not only are the mutation and the particularly elaborate selection dispensed with, but also the risk of generating undesired multiple mutations is avoided. The plasmid pSG5 is thus particularly well suited for this method. The temperature-sensitivity of pSG5 is manifested in such a way that this plasmid becomes unstable and is no longer replicated at temperatures at or above 36°C. The upper limit of the utilizable temperature range depends on the host cell: it is, for example, 38°C in S. venezuelae, 39°C - 3 - 22 8 4 4 1 in S. lividans and 45°C with S. ghanaensis. When cultures which contain pS65 or a derivative of this plasmid are incubated at a temperature of 36°C or above, the "plasmid becomes diluted out" and is no longer detectable after a few generations. The use, according to the invention, of the pSG5 replicon can thus be utilized to find genes which are homologous -to an existent gene. Thus a utilizable alternative to setting up a gene bank and screening with labeled DNA probes is available. This alternative is especially valuable when the result obtained from hybridization has not been conclusive. Another advantage of this method is that it is possible to avoid working with radioactive substances. It is also possible correspondingly to find insertion elements (IS elements) and transposons which have been taken up into the genome of the host strain investigated: If, specifically, the plasmid which has been provided only with the marker and contains no other inserted DNA is used, then homologous regions are available only if an IS element or transposon has been transferred from the chromosome to the plasmid before raising the temperature. Hence selection for the marker makes it possible to find such DNA elements. The said investigations can be carried out in accordance with the method for isolating mutants described in EP-A 0,243,856. Thus the invention is associated with a number of advantages: 1. There already exists a family of vectors which is based on the pSG5 plasmid and, because of the wide host range, has a large variety of possible uses and which has various selection markers such as resistance to neomycin, thiostrepton, kanamycin (EP-A 0,158,201) and gentamicin (EP-A 0,248,207) as well as color markers such as melanin 4 22 84 4 1 and other coloring substances or pigments (EP-A 0,257,416 and 0,257,417). 2. It is possible, by use of a plasmid which belongs to the said family of vectors and contains a marker which can be selected in E. coli, to extend the method disclosed in EP-A 0,243,856 to the use of cosmid banks and thus to the isolation of large DNA sections of about 40 kb: if the marker which can be selected in E. coli is integrated into the host chromosome, the genome of the mutants produced in this way can be transferred into a cosmid gene bank. Selection for the marker (expediently at the same time as the marker intrinsic to the cosmid) then immediately leads to the cosmid clone of interest. In this way the extremely elaborate screening by hybridization which was hitherto necessary is dispensed with. In contrast to the method disclosed in EP-A 0,243,856, it is thus possible to detect in one step large gene regions in the neighborhood of the mutated gene. Gene clusters can be isolated in this way, that is to say, for example, the genes for an entire biosynthetic pathway. Nor is there any longer a need for cleavage sites suitable for restriction enzymes to be present in the vicinity of the mutated gene. The invention is explained in detail in the examples which follow. Unless indicated otherwise, percentage data herein relate to weight. Example 1: Complete DNA isolation 0.1 g of mycelium from a 3-day old homogenized Streptomycetes culture of the strain S. ghanaensis (ATCC 14672; US Patent 3,674,866), which produces no melanin (mel"), is pelleted in a 1.5 ml Eppendorf reaction tube in an Eppendorf centrifuge for 1 min and then washed once with 0.5 ml of TE (10 mM tris-HCl, 1 mM EDTA (pH 8) containing 10% sucrose). The pellet is then resuspended in 0.5 ml of lysozyme solution (0.3 M sucrose, 25 mM tris-HCl (pH 8), 25 mM EDTA, 10 mg/ml lysozyme) and incubated at 37°C for 228441 60 min. 0.2 ml of 5% strength SDS solution is added and then the solution is thoroughly mixed and incubated at 65°C for 10 min and subsequently cooled again to room temperature. Then 100 /il of phenol/chloroform (5 g of phenol, 5 ml of chloroform, 5 mg of 8-hydroxyquinoline, 1 ml of 0.1 M tris (pH 8)) are added, and the suspension is mixed cautiously on a shaker (CR)Vortex) until it is homogeneous. The mixture is then centrifuged in an Eppendorf centrifuge for 5 min, and the upper aqueous phase is transferred into a new reaction tube. 70 pi of 3 M unbuffered sodium acetate and 700 /il of isopropanol are added to the DNA-containing solution. After mixing and incubation at room temperature for 15 minutes, the DNA is pelleted by centrifugation (5 min in an Eppendorf centrifuge), and the supernatant is removed quantitatively. The DNA is resuspended in 300 pi of TE and then incubated with 10 pi of RNase solution (50 pg of RNase/ml of H20) at 37°C for 45 min. The RNase is inactivated by 100 pi of phenol/chloroform, and the denatured proteins are pelleted (5 min in an Eppendorf centrifuge). The DNA-containing solution is again treated with isopropanol (addition of 30 pi of 3 M sodium acetate and 400 pi of isopropanol, incubation at room temperature for 15 min). The DNA pellet obtained after centrifugation is washed twice with 70% strength ethanol and again pelleted. After the DNA has been dried it is taken up in 300 pi of TE and used for the further steps. Example 2: Cleavage of the complete DNA with Sau3A 1 pg of DNA is incubated in cleavage buffer (50 mM tris-HCl (pH 8), 10 mM MgCl2, 50 mM NaCl) in the presence of 1 unit of Sau3A (manufactured by BRL-Gibco, Karlsruhe) at 37°C for 1 h. The reaction is stopped by phenol treatment, and the DNA is purified by ethanol precipitation. 6 22 8 4 4 1 Example 3: Cloning of fragments of complete DNA into the plasmid pGM4 pGM4 (EP-A 0,257,416 and 0,257,417) is completely linearized with BamHI in analogy to Example 2. The two DNA samples are mixed in cleavage buffer, heated to 70oC and adjusted to the ligase reaction conditions by addition of mercaptoethanol (final conc. 10 mM) and ATP (0.1 mM). The mixture is incubated in the presence of 1 unit of T4 DNA ligase (Boehringer Mannheim) at 14°C for 12 h. The mixture is then transformed into protoplasts of the starting strain and plated out on regeneration plates. After about 20 h, a top layer of soft agar which contains sufficient thiostrepton for the final concentration in the plate to be 50 |ig/ml is placed on the latter. Example 4: Generation and selection of mutants The transformants are incubated in S medium (Hopwood et al., "Genetic Manipulation of Streptomyces, a Laboratory Manual", The John Innes Foundation, Norwich 1985) in a< shake culture at 28°C for about 36 h. The temperature is then raised to 39°C and incubation is continued at this temperature for about 36 h. The culture is harvested sterile, washed in TE + 10% sucrose and incubated in complete medium containing thiostrepton (20 mg/1) at 39°C for a further 48 h. The mutants generated in this way are then plated out and characterized (incubation always at 39°C). Example 5: Isolation of the mutated DNA The DNA is isolated as in Example 1 from the mutants, is cut with a restriction enzyme which has no cleavage sites in the integrated plasmid, and is religated with T4 DNA ligase. This results in the integrated plasmid, which now contains the mutated gene, being formed as the only cyclic DNA capable of replication. Retransformation into a suitable strain such as S. lividans is followed by </div>

Claims

<div class="application article clearfix printTableText" id="claims"> 22 84 4 1 selection for thiostrepton resistance and isolation of the plasmid which harbors the mutated gene from the transformants. The following published Australian patent applications, which are hereby incorporated by reference, correspond to the above-mentioned European specifications: EP-B 0,158,872 EP-A 0,158,201 EP-A 0,257,416 EP-A 0,257,417 = AU-A 40,599/85 = AU-A 40,600/85 = AU-A 76,803/87 = AU-A 76,802/87 WHAT //WE CLAIM IS: - 8 - 22 8 4 4 1

1. The use of pSG5 as a temperature-sensitive plasmid.

2. The use of the pSG5 replicon for the preparation of temperature-sensitive hybrid plasmids.

3. The use of the pSG5 replicon for finding IS elements and transposons.

4. A method for the preparation of Streptomycetes mutants, for the isolation of the mutated genes and for the isolation of the corresponding wild-type gene, which comprises isolating from the starting Streptomycetes strain the complete DNA, converting it into short fragments, integrating these into a hybrid plasmid which has the pSG5 replicon, containing a marker, and transforming the resulting hybrid plasmid population into the starting strain, selecting the transf ormants by selection for the marker, eliminating the hybrid plasmids by increasing the temperature above the threshold, and selecting the mutants by renewed selection for the marker.

5. The method as claimed in claim 4, wherein the mutated genes are isolated from the selected mutants.

6. The method as claimed in claim 5, wherein the corresponding wild-type genes are isolated using the mutated genes.

7. The method as claimed in claim 5, wherein the hybrid plasmid having the pSG5 replicon contains a marker which can be selected in E. coli, and wherein a cosmid bank is used in the isolation of the mutated genes. €5 - 9 -

8. The use of pSG5 as claimed in any one of claims 1, 2 or 3 substantially as herein described or exempified.

9. A method according to claim 4 substantially as herein described or exemplified. G ■{z J '"S HOECHSjT AKTIEi sGESELLSCHAFT By Their) HENRY H By: torneys LIMITED : J • t </div>