# Patent

## Title
T7 RNA polymerase variants with cysteine-serine substitutions

## Abstract

The present disclosure provide novel variants of T7 RNA polymerase. Embodiments of T7 variants, according to the instant invention, include a Cysteine-Serine substitution on position 723 of the amino acid sequence of the T7 polypeptide. Embodiments of T7 variants according to the instant invention have a DNA-dependent RNA polymerase enzymatic activity and a reduced tendency to form intramolecular homodimers by way of oxidizing thiol groups. The amino acid substitutions within the T7 variants disclosed herein impact minimally, if at all, the RNA polymerase activity of the T7 polypeptide. Further, the mutations of the disclosed embodiments may optionally be combined with mutations which provide enhanced thermostability compared to the wild-type reference.

## Background
PRIORITY CLAIM
This application is a continuation of U.S. patent application Ser. No. 13/436,110 filed Mar. 30, 2012, which claims the benefit of European Patent Application No 11160799.0, filed Apr. 1, 2011, the disclosures of which are hereby incorporated by reference in their entirety.


SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Mar. 28, 2012, is named SEQUENCE_LISTING_27368 US.txt, and is 425,986 bytes in size.
FIELD OF THE DISCLOSURE
The present disclosure pertains generally to the fields of molecular biology and protein biochemistry. More particularly, the instant disclosure pertains to the field of enzyme engineering.
BACKGROUND OF THE DISCLOSURE
T7 RNA polymerase (E.C. 2.7.7.6.), also referred to herein as “T7 polymerase” or “T7,” is a monomeric bacteriophage encoded DNA directed RNA polymerase which catalyzes the formation of RNA in the 5′→3′ direction. In the process of initiation of transcription, T7 recognizes a specific promoter sequence, the T7 promoter. T7 consists of 883 amino acids and has a molecular weight of 99 kDa. At the amino acid sequence level, T7 is highly homologous to T3 RNA polymerase and, to a lesser extent, SP6 RNA polymerase. The three-dimensional structure of T7 is also similar to other polymerases with different template and substrate specificities, despite low sequence similarity. T7 consists of different domains, the N-terminal domain, the “thumb”, the “palm” and the “fingers” (as described in Sousa, R., and Mukherjee, S., Prog. Nucl. Acid Res. Mol. Biol. 73 (2003) 1-41).
Cloning and expression of the gene encoding T7 has been described in literature (see, U.S. Pat. No. 4,952,496, the disclosure of which is expressly incorporated by reference). Conformational changes of T7 during transcription (see, Ma, K., et. al., Proc. Nat. Acad. Sci. 102 (2005) 17612-17617), the facilitation of promoter clearance of T7 (see, Guillerez, J., et al., Proc. Natl. Acad. Sci. 102 (2005) 5958-5963) and the abortive cycling phenomenon of T7 (see, He, B., et al., J. Mol. Biol. 265 (1997) 275-288) have all been studied.
T7 has been classified as having high promoter specificity and RNA polymerase enzymatic activity, and as being useful for a variety of applications in molecular biology. In the field of recombinant protein expression, T7 is used for the high-level expression of recombinant genes in E. coli (for example, as discussed in Studier, F. W., and Moffat, B. A., J. Mol. Biol. 189 (1986) 113-130). The synthesis of defined oligoribonucleotides was described by Milligan, J. F., et al., Nucl. Aids Res. 15 (1987) 8783-8798. However, for at least some applications with which T7 RNA Polymerase may be utilized a more stable T7 RNA polymerase would be of value.
SUMMARY OF THE DISCLOSURE
According to the instant invention, novel variants of T7 polymerase are provided. According to embodiments of the invention, a T7 variant is provided which includes a Cysteine-Serine substitution on position 723 of the amino acid sequence of the T7 polypeptide. According to some embodiments, a T7 variant has a DNA-dependent RNA polymerase enzymatic activity and a reduced tendency to form intermolecular homodimers by way of oxidizing thiol groups is provided. The amino acid substitutions, according to the instant invention, have none (or at most only minimal) impact on the RNA polymerase activity of the T7 polypeptide. According to the instant disclosure, the mutations disclosed herein can optionally be combined with even further mutations, including mutations which provide enhanced thermostability compared to the wild-type reference.
According to embodiments of the present disclosure, variants of T7 RNA polymerase with Cys-Ser substitution mutations leading to improved stability are provided. Further, the instant disclosure provides combinations of several T7 RNA polymerase mutations in a single T7 variant (double-, triple-, quadruple-, multiple-mutant), with the proviso that the combined mutations lead to an even increased stability, that is to say enhanced storage characteristics. Even further, the present invention provides mutations which give rise to T7 variants which additionally exhibit enhanced stability in thermal unfolding assays.
The present invention also provides improved variants of T7 RNA polymerase by introducing mutations which reduce one or more thiol (=mercapto, =—SH, =sulfhydryl) group(s) of the enzyme while retaining enzymatic activity. For example, some embodiments of the instant disclosure include amino acid substitutions with Serine at any of the positions Cys125, Cys347, Cys492, Cys515, Cys723, Cys839, and combinations thereof.
According to some embodiments of the instant disclosure, an aqueous solution lacking a reducing agent with a thiol group is provided. The aqueous solution comprises a variant polypeptide of T7 RNA polymerase which has DNA-dependent RNA polymerase activity and a different amino acid sequence from SEQ ID NO.:2. The variant also includes a Cysteine residue at amino acid position between 510 and 530, the numbering being from the N-terminus of SEQ ID NO.:2. Further, the variant includes a Serine residue substitution for the Cysteine residue at amino acid position 723, again numbered from the N-terminus of SEQ ID NO.:2. Even further, in the aqueous solution the variant lacks homomultimer formation of intermolecular disulfide bonds.
According to some such embodiments, the variant may also include one or more of the Cysteine-Serine substitutions selected from the group consisting of Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, and Cys839Ser.
According to other such embodiments, the variant may also include one or more of the amino acid substitutions selected from the group consisting of Val426Leu, Val426Ile, Val426Phe, Ser633Val, Ser633Met, Val650Leu, Thr654Leu, Ala702Val, and Val795Ile.
Another embodiment of the instant disclosure includes a method of synthesizing a RNA molecule. Embodiments of this method include the step of providing an aqueous solution devoid of a reducing agent with a thiol group. The solution has a variant polypeptide of T7 RNA polymerase. The variant also has DNA-dependent RNA polymerase activity and an amino acid sequence different from SEQ ID NO:2. Further, the variant is devoid of homomultimer formation of intermolecular disulfide bonds when in the solution. Embodiments of this method also include the step of providing a template DNA molecule comprising a T7 promoter functionally linked to a target nucleotide sequence to be transcribed. Embodiments of this method also include the steps of contacting, within the solution, the template DNA molecule with the variant in the presence of ribonucleoside triphosphates, and incubating the solution, following the step of contacting, under conditions favoring RNA polymerase activity, thereby synthesizing the RNA molecule.
According to some such embodiments, the variant may also include one or more of the Cysteine-Serine substitutions selected from the group consisting of Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, and Cys839Ser.
According to other such embodiments, the variant may also include one or more of the amino acid substitutions selected from the group consisting of Val426Leu, Val426Ile, Val426Phe, Ser633Val, Ser633Met, Val650Leu, Thr654Leu, Ala702Val, and Val795Ile.
According to yet other embodiments of the instant disclosure, a method of producing an aqueous solution devoid of a reducing agent including a thiol group is provided. According to such embodiments, the solution comprises a variant of T7 RNA polymerase having DNA-dependent RNA polymerase activity and an amino acid sequence different from SEQ ID NO:2. The variant is devoid of homomultimer formation of intermolecular disulfide bonds when in the solution. According to such embodiments, the method comprises the step of providing the variant by substituting a Cysteine residue at amino acid position 723, the positions numbered from the N-terminus of SEQ ID NO.:2, with a Serine residue. Such embodiments also include the steps of reverse-transcribing the amino acid sequence of the variant, thereby obtaining a nucleotide sequence encoding the variant. Such embodiments also include the step of expressing a nucleic acid molecule comprising the nucleotide sequence of the variant obtained in the step of reverse transcribing in an expression system, thereby expressing a polypeptide, and purifying the polypeptide expressed in the step of expressing, by way of chromatography using an aqueous mobile phase devoid of a reducing agent including a thiol group, thereby obtaining the solution with the variant.
According to some such embodiments, the variant may also include one or more of the Cysteine-Serine substitutions selected from the group consisting of Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, and Cys839Ser.
According to other such embodiments, the variant may also include one or more of the amino acid substitutions selected from the group consisting of Val426Leu, Val426Ile, Val426Phe, Ser633Val, Ser633Met, Val650Leu, Thr654Leu, Ala702Val, and Val795Ile.



BRIEF DESCRIPTION OF THE DRAWINGS
The features of this disclosure, and the manner of attaining them, will become more apparent and the disclosure itself will be better understood by reference to the following description of embodiments of the disclosure taken in conjunction with the accompanying drawing.
FIG. 1 is a stained SDS polyacrylamide gel (following electrophoresis) having wild-type T7 RNA polymerase in both lanes 1 and 2, the T7 RNA polymerase of lane 2 was treated with reducing reagents (DTT).
FIG. 2 is a stained SDS polyacrylamide gel (following electrophoresis) having: wild-type T7 RNA polymerase without His-tag ((Lane 1); wild-type T7 RNA polymerase including His6-tag (Lane 2); T7 variant #8 [Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, Cys723Ser, Cys839Ser] including His6-tag (Lane 3); T7 variant #6 [Cys723Ser] including His6-tag (Lane 4); T7 variant #3 [Cys347Ser] including His6-tag (Lane 5); T7 variant #7 [Cys839Ser] including His6-tag (Lane 6); T7 variant #2 [Cys125Ser] including His6-tag (Lane 7); T7 variant #4 [Cys492Ser] including His6-tag (Lane 8); and T7 variant #5 [Cys515Ser] including His6-tag (Lane 9), in which no reducing agent was added prior to electrophoresis.
FIG. 3 is a stained SDS polyacrylamide gel (following electrophoresis) having: wild-type T7 RNA polymerase without His-tag ((Lane 1); wild-type T7 RNA polymerase including His6-tag (Lane 2); T7 variant #8 [Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, Cys723Ser, Cys839Ser] including His6-tag (Lane 3); T7 variant #6 [Cys723Ser] including His6-tag (Lane 4); T7 variant #3 [Cys347Ser] including His6-tag (Lane 5); T7 variant #7 [Cys839Ser] including His6-tag (Lane 6); T7 variant #2 [Cys125Ser] including His6-tag (Lane 7); T7 variant #4 [Cys492Ser] including His6-tag (Lane 8); and T7 variant #5 [Cys515Ser] including His6-tag (Lane 9), in which 10 mM DTT was added prior to electrophoresis to provide reducing conditions.



Corresponding reference characters indicate corresponding parts throughout the several views. Although the drawings represent embodiments of the present disclosure, the drawings are not necessarily to scale and certain features may be exaggerated in order to better illustrate and explain the present disclosure. The exemplifications set out herein illustrate an exemplary embodiment of the disclosure, in one form, and such exemplifications are not to be construed as limiting the scope of the disclosure in any manner.
BRIEF DESCRIPTION OF THE SEQUENCE LISTING
SEQ ID NO.: 1 is the DNA sequence encoding wild-type T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #1 in Table 3.
SEQ ID NO.: 2 is the wild-type T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #1 in Table 3.
SEQ ID NO.: 3 is the DNA sequence encoding the Cys125Ser variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #2 in Table 3.
SEQ ID NO.: 4 is the sequence of Cys125Ser variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #2 in Table 3.
SEQ ID NO.: 5 is the DNA sequence encoding the Cys347Ser variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #3 in Table 3.
SEQ ID NO.: 6 is the Cys347Ser variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #3 in Table 3.
SEQ ID NO.: 7 is the DNA sequence encoding the Cys492Ser variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #4 in Table 3.
SEQ ID NO.: 8 is Cys492Ser variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #4 in Table 3.
SEQ ID NO.: 9 is the DNA sequence encoding the Cys515Ser variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #5 in Table 3.
SEQ ID NO.: 10 is Cys515Ser variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #5 in Table 3.
SEQ ID NO.: 11 is the DNA sequence encoding the Cys723Ser variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #6 in Table 3.
SEQ ID NO.: 12 is the Cys723Ser variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #6 in Table 3.
SEQ ID NO.: 13 is the DNA sequence encoding the Cys839Ser variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #7 in Table 3.
SEQ ID NO.: 14 is Cys839Ser variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #7 in Table 3.
SEQ ID NO.: 15 is the DNA sequence encoding the Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, Cys723Ser, Cys839Ser variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #8 in Table 3.
SEQ ID NO.: 16 is Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, Cys723Ser, Cys839Ser variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #8 in Table 3.
SEQ ID NO.: 17 is the DNA sequence encoding the Val426Leu variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #9 in Table 3.
SEQ ID NO.: 18 is Val426Leu variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #9 in Table 3.
SEQ ID NO.: 19 is the DNA sequence encoding the Cys723Ser, Val426Leu variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #10 in Table 3.
SEQ ID NO.: 20 is Cys723Ser, Val426Leu variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #10 in Table 3.
SEQ ID NO.: 21 is the DNA sequence encoding the Val426Ile variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #11 in Table 3.
SEQ ID NO.: 22 is Val426Ile variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #11 in Table 3.
SEQ ID NO.: 23 is the DNA sequence encoding the Cys723Ser, Val426Ile variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #12 in Table 3.
SEQ ID NO.: 24 is Cys723Ser, Val426Ile variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #12 in Table 3.
SEQ ID NO.: 25 is the DNA sequence encoding the Val426Phe variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #13 in Table 3.
SEQ ID NO.: 26 is Val426Phe variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #13 in Table 3.
SEQ ID NO.: 27 is the DNA sequence encoding the Cys723Ser, Val426Phe variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #14 in Table 3.
SEQ ID NO.: 28 is Cys723Ser, Val426Phe variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #14 in Table 3.
SEQ ID NO.: 29 is the DNA sequence encoding the Ser633Met variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #15 in Table 3.
SEQ ID NO.: 30 is Ser633Met variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #15 in Table 3.
SEQ ID NO.: 31 is the DNA sequence encoding the Cys723Ser, Ser633Met variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #16 in Table 3.
SEQ ID NO.: 32 is the DNA sequence encoding the Cys723Ser, Ser633Met variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #16 in Table 3.
SEQ ID NO.: 33 is the DNA sequence encoding the Val650Leu variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #17 in Table 3.
SEQ ID NO.: 34 is Val650Leu variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #17 in Table 3.
SEQ ID NO.: 35 is the DNA sequence encoding the Cys723Ser, Val650Leu variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #18 in Table 3.
SEQ ID NO.: 36 is Cys723Ser, Val650Leu variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #18 in Table 3.
SEQ ID NO.: 37 is the DNA sequence encoding the Thr654Leu variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #19 in Table 3.
SEQ ID NO.: 38 is Thr654Leu variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #19 in Table 3.
SEQ ID NO.: 39 is the DNA sequence encoding the Cys723Ser, Thr654Leu variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #20 in Table 3.
SEQ ID NO.: 40 is Cys723Ser, Thr654Leu variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #20 in Table 3.
SEQ ID NO.: 41 is the DNA sequence encoding the Ala702Val variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #21 in Table 3.
SEQ ID NO.: 42 is Ala702Val variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #21 in Table 3.
SEQ ID NO.: 43 is the DNA sequence encoding the Cys723Ser, Ala702Val variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #22 in Table 3.
SEQ ID NO.: 44 is Cys723Ser, Ala702Val variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #22 in Table 3.
SEQ ID NO.: 45 is the DNA sequence encoding the Val795Ile variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #23 in Table 3.
SEQ ID NO.: 46 is Val795Ile variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #23 in Table 3.
SEQ ID NO.: 47 is the DNA sequence encoding the Cys723Ser, Val795Ile variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #24 in Table 3.
SEQ ID NO.: 48 is Cys723Ser, Val795Ile variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #24 in Table 3.
SEQ ID NO.: 49 is the DNA sequence encoding the Ala702Val, Val795Ile variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #25 in Table 3.
SEQ ID NO.: 50 is Ala702Val, Val795Ile variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #25 in Table 3.
SEQ ID NO.: 51 is the DNA sequence encoding the Cys723Ser, Ala702Val, Val795Ile variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #26 in Table 3.
SEQ ID NO.: 52 is Cys723Ser, Ala702Val, Val795Ile variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #26 in Table 3.
SEQ ID NO.: 53 is the DNA sequence encoding the Val426Leu, Ala702Val variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #27 in Table 3.
SEQ ID NO.: 54 is Val426Leu, Ala702Val variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #27 in Table 3.
SEQ ID NO.: 55 is the DNA sequence encoding the Cys723Ser, Val426Leu, Ala702Val variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #28 in Table 3.
SEQ ID NO.: 56 is Cys723Ser, Val426Leu, Ala702Val variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #28 in Table 3.
SEQ ID NO.: 57 is the DNA sequence encoding the Val426Leu, Val795Ile variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #29 in Table 3.
SEQ ID NO.: 58 is Val426Leu, Val795Ile variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #29 in Table 3.
SEQ ID NO.: 59 is the DNA sequence encoding the Cys723Ser, Val426Leu, Val795Ile variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #30 in Table 3.
SEQ ID NO.: 60 is the DNA sequence encoding the Cys723Ser, Val426Leu, Val795Ile variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #30 in Table 3.
SEQ ID NO.: 61 is the DNA sequence encoding the Val426Leu, Ala702Val, Val795Ile variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #31 in Table 3.
SEQ ID NO.: 62 is Val426Leu, Ala702Val, Val795Ile variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #31 in Table 3.
SEQ ID NO.: 63 is the DNA sequence encoding the Cys723Ser, Val426Leu, Ala702Val, Val795Ile variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #32 in Table 3.
SEQ ID NO.: 64 is Cys723Ser, Val426Leu, Ala702Val, Val795Ile variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #32 in Table 3.
SEQ ID NO.: 65 is the DNA sequence encoding the Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, Cys723Ser, Cys839Ser, Val426Leu, Ala702Val, Val795Ile variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #33 in Table 3.
SEQ ID NO.: 66 is Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, Cys723Ser, Cys839Ser, Val426Leu, Ala702Val, Val795Ile variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #33 in Table 3.
SEQ ID NO.: 67 is the DNA sequence encoding the Val426Leu, Val650Leu, Ala702Val, Val795Ile variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #34 in Table 3.
SEQ ID NO.: 68 is Val426Leu, Val650Leu, Ala702Val, Val795Ile variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #34 in Table 3.
SEQ ID NO.: 69 is the DNA sequence encoding the Cys723Ser, Val426Leu, Val650Leu, Ala702Val, Val795Ile variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #35 in Table 3.
SEQ ID NO.: 70 is Cys723Ser, Val426Leu, Val650Leu, Ala702Val, Val795Ile variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #35 in Table 3 SEQ ID NO.: 71 is the DNA sequence encoding the C125S, C347S, C492S, C515S, C723S, C839S, V426L, V650L, A702V, V7951 variant of T7 DNA-dependent RNA polymerase, including start codon encoding N-terminal methionine; corresponding to #36 in Table 3.
SEQ ID NO.: 72 is C125S, C347S, C492S, C515S, C723S, C839S, V426L, V650L, A702V, V7951 variant of T7 DNA-dependent RNA polymerase, amino acid sequence including N-terminal methionine; corresponding to #36 in Table 3.
SEQ ID NO.: 73 is the DNA encoding N-terminal Histidine (His6) tag with linker sequence, fused to the first two N-terminal amino acids of T7 (Met and Asn).
SEQ ID NO.: 74 is the Amino acid sequence of N-terminal Histidine (His6) tag with linker sequence, fused to the first two N-terminal amino acids of T7 (Met and Asn).
SEQ ID NO.: 75 is the Histidine tag (amino acids); this region may encompass 3 to 7 “His” residues.
SEQ ID NO.: 76 is the His6 tag (amino acids).
Although the sequence listing represents an embodiment of the present disclosure, the sequence listing is not to be construed as limiting the scope of the disclosure in any manner and may be modified in any manner as consistent with the instant disclosure and as set forth herein.
DETAILED DESCRIPTION OF THE EMBODIMENTS OF THE DISCLOSURE
The embodiments disclosed herein are not intended to be exhaustive or limit the disclosure to the precise form disclosed in the following detailed description. Rather, the embodiments are chosen and described so that others skilled in the art may utilize their teachings.
The instant disclosure provides the surprising and unexpected discovery that the T7 RNA polymerase Cys-Ser mutations disclosed herein do not impact equally on intramolecular disulfide bond formation of T7 polymerase. Further, in embodiments of the instant disclosure it is disclosed herein that, surprisingly, Cys723 is an important residue with regards to homomultimer formation. Further, in some embodiments Cys839 may be involved in forming disulfide bridges in homomultimers. For example, according to some embodiments of the instant disclosure, a T7 variant with only a Cys723Ser substitution, homomultimer formation is detectably absent. According to an embodiment of the instant disclosure, a T7 variant with only a C839S substitution homomultimer formation is substantially reduced. Very surprisingly, according to another embodiment of the instant disclosure, a sextuple amino acid substitution T7 variant [C125S, C347S, C492S, C515S, C723S, C839S] is indistinguishable from a T7 variant with only a C723S substitution, as far as homomultimer formation is concerned. Also surprising, the sextuple T7 variant disclosed herein and the T7 variants with only a C723S substitution or only a C839S substitution exhibit RNA polymerase activity similar to that of the wild-type T7 enzyme. As disclosed herein, amino acid substitution mutations on the positions C125, C347, C492, C515, C723, and C839 are very useful and advantageous for constructing variant T7 polymerase enzymes with reduced tendency to form multimers with disulfide bridges.
The formation of disulfide bonds can occur during or after the synthesis of certain proteins. Intramolecular disulfide bonds can significantly contribute to the stability of proteins. Disulfide bond formation also occurs between different protein molecules. Cysteine residues involved in this process have to be located at the surface of the protein molecule and have to be solvent exposed. Additionally, the cysteine residues have to be in a suitable geometry and distance to each other to facilitate the formation of a disulfide bond.
By way of forming one or more intermolecular disulfide bond(s) between proteins, di-, tri-, tetra-, penta-, and higher degree of multimeric protein complexes can be generated. However, uncontrolled and unfavourable formation of such protein complexes by disulfide bonds under artificial conditions (e.g. in purified preparations of proteins) can impact on biological (e.g. enzymatic) activity or functionality. Therefore, efforts are made to keep proteins under reducing conditions. A common method is the addition of reducing agents to the storage buffers; examples for such reducing agents are mercaptoethanol, dithiothreitol (DTT), dithioerythritol (DTE) and others. However, thiol group reducing agents have a limited shelf life as they themselves are oxidized by molecular oxygen. As a consequence, thiol reducing agents are losing their protective activity over time, and oxidation of cysteine residues together with disulfide bond formation can again take place.
If a protein sample contains a mixture of different polypeptides or if the sample is a crude extract, formation of multimers is possible between molecules of different protein species (heteromultimers). If the mixture contains several purified polypeptides of defined activities, formation of heteromultimers between these proteins can negatively influence such activities, affecting single polypeptides separately or all members of the sample.
According to the instant disclosure, T7 RNA polymerase (such as the wild-type T7 RNA polymerase) contains 12 cysteines each having free thiol as functional group. When the thiol groups of two cysteine residues are brought near each other, an oxidation reaction can generate a cystine unit with a disulfide bond (—S—S—). Storage of T7 RNA polymerase in the absence of thiol reducing agents results in reduced enzymatic activity. Reduction of activity is correlated with the formation of dimers, trimers and even multimers of the enzyme. The kinetics of disulfide bond formation are strongly dependent on parameters like protein concentration, reaction time, temperature and the presence or absence of oxidizing reagents. Therefore, in practice, the percentage of multimers present in a sample can vary depending on the origin, age and composition of the sample. Even during the purification procedure intermolecular disulfide bond formation can be observed sometimes.
T7 multimers such as dimers, trimers or even higher degree multimers, may exhibit decreased polymerase activity, possibly due to a reduced accessibility of the active sites. A reduced flexibility of the individual polypeptide backbones could also negatively impact enzymatic function. Although polymerase activity can be restored by adding freshly prepared —SH reagents, it is required to continuously monitor residual activity of the enzyme. In order to safeguard and/or regain enzymatic activity and/or provide an enzyme preparation with defined T7 polymerase activity, it is further necessary to frequently manipulate the material, for example by removing and analyzing samples and reacting T7 preparations with reducing agents, etc.
DTNB [5,5′-dithiobis-(2-nitrobenzoic acid), also known as Ellman's reagent] is a chemical which can be used to quantify the number or concentration of thiol groups in a polypeptide. A thiol group reacts with DTNB, cleaving the disulfide bond to give 2-nitro-5-thiobenzoate (NTB−), which ionizes to the NTB2− dianion in water at neutral and alkaline pH. The NTB2− ion has a yellow color and can be determined, for example, spectrophotometrically. The reaction of thiol groups and DTNB is rapid and stoichiometric, with one mole of thiol releasing one mole of NTB (for example, the reactivity of T7 RNA polymerase with DTNB has been previously determined as disclosed in Mukherjee, S., et al., Cell 110 (2002) 81-91). Per one native polypeptide of wild-type T7 polymerase enzyme the equivalent of about 2 reactive Cys residues were found but for the denatured wild-type T7 enzyme the number of reactive Cys residues determined was 12.
According to the instant disclosure, in at least some applications with which T7 RNA Polymerase may be utilized, such as in vitro transcription and in vitro amplification methods including Nucleic Acid Sequence Based Amplification (“NASBA”), Transcription mediated amplification (“TMA”), and other related methods and applications, increasing the stability of the T7 RNA polymerase would be beneficial. For example, it would be beneficial to have a T7 RNA polymerase with an increased storage time wherein any loss of polymerase enzymatic activity is minimized and/or a T7 RNA polymerase which can be stored at room temperature with only minor or no loss of enzymatic activity. Also, combining the technical features leading to enhanced storage characteristics with other features leading to enhanced thermostability (e.g., higher reaction temperatures of isothermal amplification) could allow the amplification of RNA having secondary structures. It has also been shown with the polymerase chain reaction (PCR) technology that high annealing temperatures allow the specific hybridization of a primer to its target resulting in a highly specific amplification. With the same advantage, more thermostable enzymes could in principle also be applied to isothermal amplifications.
According to some embodiments of the instant disclosure, a T7 RNA polymerase variant having improved stability, for example enhanced storage characteristics and a reduced tendency to form multimers with disulfide bridges, is provided. According to some embodiments, the T7 RNA polymerase variants provided herein combine the enhanced stability features with polymerase activity at reaction temperatures higher than those of the wild-type T7 enzyme.
According to the present disclosure, Cys723 is a cysteine residue of T7 polymerase which contributes to disulfide bond formation. For example, according to the instant disclosure, Cys723Ser variants, even after long term storage of such purified variants, analysis by way of SDS gel electrophoresis reveals only a single band under non-reducing conditions. This indicates that the homodimer formation is completely suppressed by the introduction of this single specific mutation. No other Cys-Ser substitution was found to produce a similar effect in a T7 variant with RNA polymerase activity, i.e. in an active enzyme.
As also disclosed herein, the combination of six mutations within a T7 gene results in an active enzyme. The six-fold mutant (Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, Cys723Ser, Cys839Ser) also shows a single band under non-reducing conditions (and reducing conditions, too). This indicates that dimer formation can be suppressed completely by the introduction of Cys-Ser substitution mutations according to the invention.
The present invention provides novel variants of T7 polymerase, variants which are characterized by a different composition of amino acids compared to the wild-type T7 RNA polymerase polypeptide (wild-type reference). Such a “variant” is an allelic form of the wild-type T7 protein, wherein the T7 variant is generated by way of amino acid substitution. A T7 variant according to the invention is further characterized by a DNA-dependent RNA polymerase enzymatic activity, and a reduced tendency to form intramolecular dimers by way of oxidizing thiol groups. The identified amino acid substitutions according to the invention appear to impact only minimally, if at all, on the biological function of the T7 polymerase polypeptide, including RNA polymerase activity. The mutations can optionally be combined with even further mutations, including mutations which provide enhanced thermostability compared to the wild-type reference.
Certain terms are used with particular meaning or are defined for the first time in this description of the present invention. For the purposes of the invention, the terms used are defined by their art-accepted definitions, when such exist, except that when those definitions conflict or partially conflict with the definitions set forth below. In the event of a conflict in definition, the meaning of a term is first defined by any of the definitions set forth in this document.
The term “comprising” is used in the description of the invention and in the claims to mean “including, but not necessarily limited to”.
The articles “a” and “an” are used herein to refer to one or to more than one (i.e. to “one or more” or “at least one”) of the grammatical object of the article. By way of example, “an amino acid” means one amino acid or more than one amino acid.
If not stated otherwise, it is understood that the term “about” in combination with a numerical value n (“about n”) indicates a value x in the interval given by the numerical value ±5% of the value, i.e. n−0.05*n≦x≦n+0.05*n. In case the term “about” in combination with a numerical value n describes a preferred embodiment of the invention, the value of n is most preferred, if not indicated otherwise.
A nucleotide sequence “encodes” a peptide or polypeptide when at least a portion of the nucleic acid, or its complement, can be directly translated to provide the amino acid sequence of the peptide or protein, or when the isolated nucleic acid can be used, alone or as part of an expression vector, to express the peptide or protein in vitro, in a prokaryotic host cell, or in a eukaryotic host cell.
Where a nucleotide sequence is single-stranded, it is to be understood that the complementary sequence of that nucleotide sequence is also included within the scope of the present invention.
The coding portion of a nucleotide sequence encoding a peptide or a polypeptide begins with a start codon encoding Methionine which thus becomes the N-terminal amino acid of the primary translation product. As part of post-translational processes, the N-terminal Methionine is frequently cleaved off, e.g. by a Methionine aminopeptidase which is a ubiquituous enzyme. In such a case, the primary translation product may give rise to a mixture comprising members without N-terminal Methionine and members retaining this amino acid as N-terminus. It is also possible that the form of the enzyme without N-terminal Methionine is the only one which can be isolated. However, the amino acid sequences of the wild-type T7 polymerase and the T7 variants according to the invention are described in the sequence listing including N-terminal Methionine. But the present invention also encompasses the T7 variants which do not include N-terminal Methionine.
For purposes of shorthand designation of T7 polymerase variants described herein, it is noted that for each mutation a number refers to the amino acid residue/position along the reference amino acid sequence of the wild-type T7 polymerase protein given in SEQ ID NO:2. Amino acid identification uses the three-letter abbreviations as well as the single-letter alphabet of amino acids, i.e., Asp D Aspartic acid, Ile I Isoleucine, Thr T Threonine, Leu L Leucine, Ser S Serine, Tyr Y Tyrosine, Glu E Glutamic acid, Phe F Phenylalanine, Pro P Proline, His H Histidine, Gly G Glycine, Lys K Lysine, Ala A Alanine, Arg R Arginine, Cys C Cysteine, Trp W Tryptophan, Val V Valine, Gln Q Glutamine, Met M Methionine, Asn N Asparagine. An amino acid at a particular position in an amino acid sequence may be given by its three-letter abbreviation and a number. For example, “Cys723” or “C723” denote the Cysteine residue at amino acid position 723 in SEQ ID NO:2. In any T7 mutant and/or T7 variant disclosed herein, a substitution by a different amino acid may be given as the three-letter abbreviation added after the number indicating the position. For example, “Cys723Ser” (=[Cys723Ser]) or “C723S” (=[C723S]) denotes the substitution of Cysteine (Cys) at position 723 in SEQ ID NO:2 by Serine (Ser) (see #6 of Table 3). A Cys723Ser (=C723S) substitution results in an amino acid sequence as given in SEQ ID NO:12, encoded by the nucleotide sequence of SEQ ID NO:11. Exemplary further amino acid substitutions according to the instant disclosure are disclosed in Table 1a below (see Example 1). According to some embodiments, variants may include a plurality (for example 2 to 4) amino acid substitutions. Exemplary embodiments may include amino acid substitution combinations having one or more mutations as listed in Table 1a and Table 1b.
The term “polypeptide” or “protein” denotes a polymer composed of a plurality of amino acid monomers joined by peptide bonds. According to some embodiments, the polymer may comprise 50 or more monomers. For example, polypeptide or protein according to the instant invention comprises a T7 variant. A “peptide bond” is a covalent bond between a first amino acid and a second amino acid in which the α-amino group of the first amino acid is bonded to the α-carboxyl group of the second amino acid.
A “multimer” in the context of the present invention is understood as being a conjugate formed by covalently linking two or more (=a plurality of) members, each member being a polypeptide with one or more reactive and sterically accessible thiol groups (e.g. but not limited to Cys residues). After formation of the conjugate, two or more members are linked by at least one disulfide (—S—S—) bridge. Adjacent members are linked by one or more disulfide bridge(s), and members may be linked to other members by additional disulfide bridges. A conjugate with identical members (i.e. members of the same species of polypeptide) is also referred to as a homomultimer. Depending on the number of individual members linked in the conjugate, the multimer may be referred to as a dimer, trimer, tetramer, pentamer, hexamer, etc. A heteromultimer contains at least two different species of polypeptide.
A “reducing agent with a thiol group”, also referred to as a “—SH reagent” denotes a reducing agent capable of preventing the formation of a disulfide bond of two —SH group-containing residues of one or more polypeptides. For example, according to the instant disclosure, the reducing agent with a thiol group is capable of preventing multimer formation of a T7 polypeptide with a further T7 polypeptide or the polypeptide of another species containing an —SH group. Exemplary —SH reagents within this definition include, but are not limited to, mercaptoethanol, dithiothreitol (DTT), dithioerythritol (DTE).
Illustrative T7 variants of the instant invention also comprise fusion proteins with an affinity tag such as, but not limited to, a Histidine tag (His-tag). A His-tag is an amino acid sequence containing several, for example, 3 to 7 consecutive Histidines. An illustrative embodiment of the instant disclosure include 6 consecutive Histidines. In a His-tag sequence the Histidines represent the essential portion. But facultatively there are few additional amino acids comprised in the His-tag. For example, a N-terminal T7 sequence including a His-tag can comprise the sequence N-Met His His His His His His Gly Ser-. For example, SEQ ID NO:74 comprises an illustrative embodiment of the instant disclosure including the foregoing amino acid sequence. In the present exemplary His-tag the amino acids Gly and Ser form a linker to the N-terminus of the T7 variant. The linker amino acids are part of the His-tag and typically arise as a cloning artifact of the nucleotide sequence encoding the His-tag (e.g. SEQ ID NO:73). The linker sequence in the His-tag may comprise 1 to 5 amino acids, for example, although the linker sequence may comprise greater than 5 amino acids.
According to embodiments of the instant invention, the N-terminal Methionine of a T7 variant may be replaced by a His-tag. Alternatively, the N-terminal sequence of the T7 variant, according to embodiments of the instant invention, may be extended by the His-tag. In such a case, the N-terminus of the primary translation product of the T7 variant comprises a N-terminal Methionine followed by the His-tag, followed by the Methionine encoded by the start codon of the original T7 encoding nucleotide sequence.
Purification of a His-tagged T7 wild-type or variant polypeptide may be efficiently performed by immobilized metal affinity chromatography, such as is employed in the purification of recombinant proteins containing a short affinity-tag consisting of Histidine residues (His-tag). Immobilized metal-affinity chromatography (described by Porath, J., et al., Nature 258 (1975) 598-599, for example) is based on the interaction between a transition metal ion (Co2+, Ni2+, Cu2+, Zn2+) immobilized on a particulate metal chelating affinity matrix and specific amino acid side chains. Histidine is the amino acid that exhibits the strongest interaction with immobilized metal ion matrices, as electron donor groups on the Histidine imidazole ring readily form coordination bonds with the immobilized transition metal.
A “vector” is a DNA which can comprise, i.e. carry, and maintain a DNA fragment according to the instant invention, including, for example, phages and plasmids. These terms are generally understood by those of skill in the art of genetic engineering for example. The term “expression cassette” denotes a nucleotide sequence encoding a pre-protein, operably linked to a promoter and a terminator. As for vectors containing an expression cassette, the terms “vector” and “expression vector” are used as synonyms.
The term “oligonucleotide” is used for a nucleic acid molecule, DNA (or RNA), generally having less than 100 nucleotides in length. An oligonucleotide may be, for example, about 75, about 50 or even less nucleotides in length.
“Transformation” means introducing DNA into an organism, i.e. a host organism, so that the DNA is replicable, either as an extrachromosomal element or by chromosomal integration.
The term “expression” and the verb “to express” denote transcription of DNA sequences and/or the translation of the transcribed mRNA in a host organism resulting in a pre-protein, i.e. not including post-translational processes.
A “promoter” is a regulatory nucleotide sequence that stimulates transcription. These terms are understood by those of skill in the art of genetic engineering and the like, for example. Like a promoter, a “promoter element” stimulates transcription but constitutes a sub-fragment of a larger promoter sequence.
The term “operably linked” refers to the association of two or more nucleic acid fragments on a single vector so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence, i.e. a nucleotide sequence encoding a protein or a pre-protein, when it is capable of affecting the expression of that coding sequence, i.e., that the coding sequence is under the transcriptional control of the promoter.
An objective of the present invention was to provide new mutants of T7 RNA polymerase comprising no, or substantially reduced, tendency to form intramolecular disulfide bonds and generate multimers. High resolution x-ray structures of T7 RNA polymerase were carefully inspected for the identification of cysteine residues in the protein structures which may allow for introduction of mutations therein.
According to embodiments of the instant disclosure, and as disclosed herein, one or more identified cysteine residues were replaced by Serine residues. Cys-Ser substitutions were initially created as single mutations and thereafter, several different (up to six) Cys-Ser substitutions were combined in various separate coding sequences of embodiments of the T7 variants disclosed herein.
The designed T7 variants were synthesized, cloned, expressed and purified. The activity and the capability of the mutant enzymes to form multimers were examined and compared with the wild-type enzyme. It was surprisingly found that not all but only certain variants have a substantially reduced tendency to form disulfide-linked intramolecular homomultimers; that is to say, only certain T7 variants remain monomeric upon long term storage, even in the presence of oxygen, without having the requirement to be treated repeatedly with SH-reagents.
It was another surprising finding that Cys-Ser substitutions identified by the present invention do not seem to have a negative impact on RNA polymerase activity. To the contrary, Cys-Ser substitutions according to the invention can even be combined with further amino acid substitutions, e.g. with mutations which increase thermal stability of T7 RNA polymerase.
According to embodiments of the instant invention, a polypeptide comprising an improved variant of T7 RNA polymerase (T7 variant) is provided, the T7 variant having the properties of (i) DNA-dependent RNA polymerase activity, and (ii) a different composition of amino acids compared to the 883-amino acid T7 RNA polymerase polypeptide of SEQ ID NO:2 (wild-type reference). According to some such embodiments, the improvement of the T7 variant may be attributed to the absence in aqueous solution of homomultimer formation as a result of an intermolecular disulfide bond(s), wherein at a position selected from 510 and 530 of the T7 variant, numbered from the N-terminus of the wild-type reference, a Cysteine residue is present, and wherein the T7 variant comprises one or more amino acid substitution(s) of which one (or the first) is at position 723 where Serine substitutes for the Cysteine residue (Cys723Ser).
Experimental analysis involved the introduction, at selected positions, of amino acid substitutions in the T7 polypeptide. For example, the amino acids Cysteine and Serine differ only in that the sulfur atom of the former is replaced by oxygen in the latter. However, the electronegativity of the oxygen atom provides the side chain of Serine with an increased polar effect, when compared to the SH-group containing side chain of Cysteine. As such, one or more Cys-Ser substitutions change the physico-chemicals properties of a T7 variant.
One method for protein engineering includes the modification of enzyme-encoding nucleotide sequences, but requires knowledge of the structure of an enzyme and detailed biochemical data concerning the principles underlying its function and stability. Examples of improvements in protein properties, according to embodiments of the instant disclosure, include enhanced specificity, altered substrate spectrum, and thermostability, for example.
In yet more detail, the present disclosure embodies the following items.

    1. An aqueous solution in which a reducing agent with a thiol group is absent, the aqueous solution comprising a polypeptide, the polypeptide comprising a variant of T7 RNA polymerase (T7 variant), the T7 variant having the properties of (i) DNA-dependent RNA polymerase activity, and (ii) a different composition of amino acids compared to the 883-amino acid T7 RNA polymerase polypeptide of SEQ ID NO:2 (wild-type reference),
    
        wherein at a position selected from 510 and 530 of the T7 variant, numbered from the N-terminus of the wild-type reference, a Cysteine residue is present,
        wherein the T7 variant comprises one or more amino acid substitution(s) of which one (or the first) is at position 723 where Serine substitutes for the Cysteine residue (Cys723Ser),
        and wherein in the aqueous solution homomultimer formation of the T7 variant as a result of one or more intermolecular disulfide bond(s) is absent.
    
    
    2. The aqueous solution according to item 1, wherein in the polypeptide the number of substituted amino acids in the T7 variant is 1 to 10.
    3. The aqueous solution according to item 2, wherein in the polypeptide the T7 variant further comprises a Cysteine-Serine substitution selected from the group consisting of Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, and Cys839Ser.
    4. The aqueous solution according to any of the items 2 and 3, wherein in the polypeptide the T7 variant further comprises an amino acid substitution selected from the group consisting of Val426Leu, Val426Ile, Val426Phe, Ser633Val, Ser633Met, Val650Leu, Thr654Leu, Ala702Val, and Val795Ile.
    5. The aqueous solution according to item 4, wherein in the polypeptide the T7 variant comprises the amino acid substitutions Val426Leu, Val650Leu, Ala702Val, and Val795Ile.
    6. The aqueous solution according to item 4, wherein in the polypeptide the T7 variant comprises the amino acid substitutions Val426Leu, Ala702Val, and Val795Ile.
    7. The aqueous solution according to any of the items 1 to 6, wherein the polypeptide comprises the T7 variant and an N-terminal His-tag.
    8. The aqueous solution according to any of the items 1 to 7, wherein the polypeptide comprises the T7 variant with an N-terminal Methionine.
    9. A method to produce an aqueous solution with a polypeptide comprising a variant of T7 RNA polymerase (T7 variant), the T7 variant having the properties of (i) DNA-dependent RNA polymerase activity, and (ii) a different composition of amino acids compared to the 883-amino acid T7 RNA polymerase polypeptide of SEQ ID NO:2 (wild-type reference), wherein in the aqueous solution homomultimer formation as a result of one or more intermolecular disulfide bond(s) is absent, the method comprising the steps of
    
        (a) providing the T7 variant by substituting in the wild-type reference Cys723, numbered from the N-terminus, with Serine (Cys723Ser);
        (b) optionally further including in the T7 variant one or more amino acid substitution(s) selected from the group consisting of Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, and Cys839Ser;
        (c) optionally further including in the T7 variant one or more amino acid substitution(s) selected from the group consisting of Val426Leu, Val426Ile, Val426Phe, Ser633Val, Ser633Met, Val650Leu, Thr654Leu, Ala702Val, and Val795Ile;
        (d) reverse-transcribing the amino acid sequence of the polypeptide, the polypeptide comprising the T7 variant obtained in steps (a), (b), and (c), thereby obtaining a nucleotide sequence encoding the polypeptide;
        (e) expressing a nucleic acid molecule comprising the nucleotide sequence of step (d) in an expression system, and subsequently purifying the expressed polypeptide from the expression system by way of chromatography using an aqueous mobile phase in which a reducing agent with a thiol group is absent;
        thereby obtaining in step (e) an aqueous solution with the polypeptide comprising the T7 variant.
    
    
    10. The method according to item 9, wherein the aqueous solution obtained in step (e) is stored in the absence of a reducing agent with a thiol group.
    11. The method according to any of the items 9 and 10, wherein an amount of about 1 μg to 3 μg of the purified T7 variant protein from the aqueous solution is detectably free of homomultimers as determined by SDS polyacrylamide electrophoresis and staining of the electrophoresed gel with the Simply Blue Safe Stain Kit from Invitrogen.
    12. A method to synthesize a RNA molecule, comprising the steps of
    
        (a) providing an aqueous solution with a variant polypeptide of T7 RNA polymerase (T7 variant) according to any of the items 1 to 8;
        (b) providing a template DNA molecule comprising a T7 promoter, the T7 promoter being functionally linked to a target nucleotide sequence to be transcribed;
        (c) contacting in the aqueous solution the template DNA of step (b) with the T7 variant of step (a) in the presence of ribonucleoside triphosphates, thereby forming a reaction mixture;
        (d) incubating the reaction mixture under conditions permitting RNA polymerase activity;
        thereby synthesizing the RNA molecule.
    
    
    13. A reaction mixture comprising an aqueous solution with a variant polypeptide of T7 RNA polymerase (T7 variant) according to any of the items 1 to 8, wherein the aqueous solution further comprises a template DNA molecule comprising a T7 promoter functionally linked to a target nucleotide sequence to be transcribed, and ribonucleoside triphosphates.
    14. A kit comprising, in separate containers, an aqueous solution with a variant polypeptide of T7 RNA polymerase (T7 variant) according to any of the items 1 to 8 and a buffer with one or more ribonucleoside triphosphates.
    15. A polypeptide comprising an improved variant of T7 RNA polymerase (T7 variant), the T7 variant having the properties of (i) DNA-dependent RNA polymerase activity, and (ii) a different composition of amino acids compared to the 883-amino acid T7 RNA polymerase polypeptide of SEQ ID NO:2 (wild-type reference), and the improvement of the T7 variant being the absence in aqueous solution of homomultimer formation as a result of an intermolecular disulfide bond(s),
    
        wherein at a position selected from 510 and 530 of the T7 variant, numbered from the N-terminus of the wild-type reference, a Cysteine residue is present, and
        wherein the T7 variant comprises one or more amino acid substitution(s) of which one (or the first) is at position 723 where Serine substitutes for the Cysteine residue (Cys723Ser).
    
    
    16. The polypeptide according to item 15, wherein the number of substituted amino acids in the T7 variant is 1 to 10.
    17. The polypeptide according to item 16, wherein the T7 variant further comprises a Cysteine-Serine substitution selected from the group consisting of Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, and Cys839Ser.
    18. The polypeptide according to any of the items 15 to 17, wherein the aqueous solution is detectably free of homomultimers as determined by SDS polyacrylamide electrophoresis of up to about 3 μg protein (preferred about 2 μg to about 3 μg protein, more preferred up to about 2.9 μg) of the T7 variant polypeptide in purified form, and staining of the electrophoresed gel with the Simply Blue Safe Stain Kit (Invitrogen).
    19. The polypeptide according to any of the items 16 to 18, wherein the T7 variant further comprises an amino acid substitution selected from the group consisting of Val426Leu, Val426Ile, Val426Phe, Ser633Val, Ser633Met, Val650Leu, Thr654Leu, Ala702Val, and Val795Ile.
    20. The polypeptide according to item 19, wherein the T7 variant comprises the amino acid substitutions Val426Leu, Val650Leu, Ala702Val, and Val795Ile.
    21. The polypeptide according to item 19, wherein the T7 variant comprises the amino acid substitutions Val426Leu, Ala702Val, and Val795Ile.
    22. The polypeptide according to any of the items 15 to 21, wherein the polypeptide comprises the T7 variant and an N-terminal His-tag.
    23. The polypeptide according to any of the items 15 to 22, wherein the polypeptide comprises the T7 variant with an N-terminal Methionine.
    24. The polypeptide according to any of the items 15 to 23 in an aqueous solution.
    25. The polypeptide according to item 24, wherein in the aqueous solution a reducing agent with a thiol group is absent.
    26. A method to produce a polypeptide comprising an improved variant of T7 RNA polymerase (T7 variant), the T7 variant having the properties of (i) DNA-dependent RNA polymerase activity, and (ii) a different composition of amino acids compared to the 883-amino acid T7 RNA polymerase polypeptide of SEQ ID NO:2 (wild-type reference), and the improvement of the T7 variant being the absence in aqueous solution of homomultimer formation as a result of an intermolecular disulfide bond(s), the method comprising the steps of
    
        (a) providing the T7 variant by substituting in the wild-type reference Cys723, numbered from the N-terminus, with Serine (Cys723Ser);
        (b) optionally further including in the T7 variant one or more amino acid substitution(s) selected from the group consisting of Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, and Cys839Ser;
        (c) optionally further including in the T7 variant one or more amino acid substitution(s);
        (d) reverse-transcribing the amino acid sequence of the polypeptide, the polypeptide comprising the T7 variant obtained in steps (a), (b), and (c), thereby obtaining a nucleotide sequence encoding the polypeptide;
        (e) expressing a nucleic acid molecule comprising the nucleotide sequence of step (d) in an expression system, and isolating the expressed polypeptide from the expression system;
        thereby producing the polypeptide.
    
    
    27. The method according to item 26, wherein in step (c) the one or more amino acid substitution(s) is/are selected from the group consisting of Val426Leu, Val426Ile, Val426Phe, Ser633Val, Ser633Met, Val650Leu, Thr654Leu, Ala702Val, and Val795Ile.
    28. A method to produce a nucleic acid molecule with a nucleotide sequence encoding an improved variant of T7 RNA polymerase (T7 variant), the T7 variant having the properties of (i) DNA-dependent RNA polymerase activity, and (ii) a different composition of amino acids compared to the 883-amino acid T7 RNA polymerase polypeptide of SEQ ID NO:2 (wild-type reference), and the improvement of the T7 variant being the absence in aqueous solution of homomultimer formation as a result of an intermolecular disulfide bond(s), the method comprising the steps of
    
        (a) reverse transcribing an amino acid sequence of a polypeptide according to any of the items 15 to 23 or an amino acid sequence of a polypeptide obtainable by the method according to item 26 or item 27, thereby obtaining a nucleic acid sequence; followed by
        (b) synthesizing a nucleic acid molecule with the nucleic acid sequence obtained after performing step (a);
        thereby producing the nucleic acid molecule encoding the T7 variant.
    
    
    29. A nucleic acid molecule comprising a nucleotide sequence selected from a member of the group consisting of SEQ ID NOs: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, and 71.
    30. An expression vector comprising one or more nucleotide sequences capable of controlling transcription and/or translation and functionally linked to (a) a nucleic acid molecule obtainable by the method of item 28, or (b) a nucleic acid according to item 29.
    31. A host organism capable of recombinant expression of a polypeptide, wherein the host organism is transformed with an expression vector according to item 30.
    32. The host organism according to item 31, wherein the host organism is Escherichia coli. 
    33. A method to synthesize a RNA molecule, comprising the steps of
    
        (a) providing a variant polypeptide of T7 RNA polymerase (T7 variant) according to any of the items 15 to 23;
        (b) providing a template DNA molecule comprising a T7 promoter, the T7 promoter being functionally linked to a target nucleotide sequence to be transcribed;
        (c) contacting in aqueous solution the template DNA of step (b) with the T7 variant of step (a) in the presence of ribonucleoside triphosphates, thereby forming a reaction mixture;
        (d) incubating the reaction mixture under conditions permitting RNA polymerase activity;
        thereby synthesizing the RNA molecule.
    
    
    34. The method according to item 33, wherein in any of the steps (a), (b), (c), and (d) a reducing agent with a thiol group is absent.
    35. The method according to item 33, wherein in any of the steps (a), (b), (c), and (d) a reducing agent selected from mercaptoethanol, dithiothreitol, dithioerythritol is absent.
    36. A reaction mixture comprising in aqueous solution a template DNA molecule comprising a T7 promoter functionally linked to a target nucleotide sequence to be transcribed, ribonucleoside triphosphates, and a variant polypeptide of T7 RNA polymerase (T7 variant) according to any of the items 15 to 23, and wherein in the reaction mixture a reducing agent with a thiol group is absent.
    37. A reaction mixture comprising in aqueous solution a template DNA molecule comprising a T7 promoter functionally linked to a target nucleotide sequence to be transcribed, ribonucleoside triphosphates, and a variant polypeptide of T7 RNA polymerase (T7 variant) according to any of the items 15 to 23, and wherein in the reaction mixture a reducing agent selected from mercaptoethanol, dithiothreitol, dithioerythritol is absent.
    38. A kit comprising, in separate containers, a variant polypeptide of T7 RNA polymerase (T7 variant) according to any of the items 15 to 23 and a buffer with one or more ribonucleoside triphosphates, wherein the T7 variant is in aqueous solution, wherein in the aqueous solution mixture a reducing agent with a thiol group is absent.
    39. A kit comprising, in separate containers, a variant polypeptide of T7 RNA polymerase (T7 variant) according to any of the items 15 to 23 and a buffer with one or more ribonucleoside triphosphates, wherein the T7 variant is in aqueous solution, wherein in the aqueous solution mixture a reducing agent selected from mercaptoethanol, dithiothreitol, dithioerythritol is absent.
    40. A variant T7 RNA polymerase polypeptide having DNA-dependent RNA polymerase activity and an amino acid sequence different from SEQ ID NO.:2, the variant including a Cysteine residue at amino acid position between 510 and 530, numbered from the N-terminus of SEQ ID NO.:2, and a Serine residue substitution for the Cysteine residue at amino acid position 723, numbered from the N-terminus of SEQ ID NO.:2, wherein when in the aqueous solution the variant is devoid of homomultimer formation of intermolecular disulfide bond(s).
    41. The variant of claim 40, wherein the variant comprises at least 2 and less than or equal to 10 amino acid substitutions as compared to SEQ ID NO.:2.
    42. The variant of claim 40, wherein the variant further comprises a Cysteine-Serine substitution selected from the group consisting of Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, and Cys839Ser.
    43. The variant of claim 40, wherein the variant further comprises an amino acid substitution selected from the group consisting of Val426Leu, Val426Ile, Val426Phe, Ser633Val, Ser633Met, Val650Leu, Thr654Leu, Ala702Val, and Val795Ile.
    44. The variant of claim 40, wherein the variant comprises amino acid substitutions Val426Leu, Val650Leu, Ala702Val, and Val795Ile.
    45. The variant of claim 40, wherein the variant comprises amino acid substitutions Val426Leu, Ala702Val, and Val795Ile.
    46. The variant of claim 40, wherein an N-terminal His-tag is linked to the variant.
    47. The variant of claim 40, wherein an N-terminal Methionine is linked to the variant.


The following examples, sequence listing, and figures are provided for the purpose of demonstrating various embodiments of the instant disclosure and aiding in an understanding of the present disclosure, the true scope of which is set forth in the appended claims. These examples are not intended to, and should not be understood as, limiting the scope or spirit of the instant disclosure in any way. It should also be understood that modifications can be made in the procedures set forth without departing from the spirit of the disclosure.
EXAMPLES
Example 1. Design of Amino Acid Exchange Mutations in the T7 Polypeptide
X-ray structures of T7 RNA polymerase deposited in the Protein Data Bank (http://www.wwpdb.org/pdb; codes: 1cez [referring to Cheetham, G. M. T., et al., Nature 399 (1999) 80-83], and 1s77 [referring to Yin, Y. W., and Steitz, T. A., Cell 116 (2004) 393-404]) were inspected to identify candidate sites for the introduction of mutations. To this end, cysteine residues were localized in three dimensional models and Cys residues on the surface of the T7 polypeptide which in principle could be accessible for the formation of intramolecular disulfide bonds were identified. Further, candidate amino acid residues were identified with the goal in mind to increase the stability of the protein.
Selected positions of the T7 wild-type amino acid sequence (according to SEQ ID NO:2) are shown in Table 1a which show candidate Cysteines. Table 1b provides amino acid substitution mutations expected to increase the stability of the T7 polymerase protein. The underlying rationale of the design of the mutations is also indicated, in order to increase the stability of a variant T7 polypeptide versus the wildtype reference. Thus, most of the substituting amino acids were selected either to fill hydrophobic cavities in the core or to stabilize loops located at the surface of the enzyme.







TABLE 1a







Amino Acid Mutations of T7RNA Polymerase: Design of an


Enzyme with Reduced Tendency to Form Multimers Linked by 


Intramolecular Disulfide Bridges.











Cys residue in WT T7 polypeptide, 





position in amino acid sequence 
Predicted
Proposed



(SEQ ID NO: 2)
localization
mutation







125
surface
Ser



216
buried
—



271
buried
—



347
surface
Ser



467
buried
—



492
surface
Ser



510
buried
—



515
surface
Ser



530
buried
—



540
buried
—



723
surface
Ser



839
surface
Ser

















TABLE 1b







Amino Acid Mutations of T7 RNA Polymerase: Design of an Enzyme 


with Increased Thermostability.










Amino acid,





WT
Position
Mutation
Rationale





Val
426
Leu, Ile, Phe, 
Fill cavity in protein




Trp
core


Ser
633
Val, Leu, Met
Stabilize loop


Val
650
Leu
Stabilize loop


Thr
654
Leu
Stabilize loop


Ala
702
Val
Fill cavity in protein





core


Val
795
Ile
Fill cavity in protein





core









In order to provide a coding sequence for any of the T7 mutants presented herein, the nucleotide sequence of SEQ ID NO:1 encoding the T7 wild type reference polypeptide was used as a basis. The nucleotide codons corresponding to the amino acid residues at the positions indicated in Tables 1a and 1b were mutated, in order to encode the changed amino acid at the respective position. Mutations were preferably designed in accordance with the codon usage bias of E. coli class II genes (as described in Hénaut, A., and Danchin, A., Analysis and Predictions from Escherichia coli sequences. Escherichia coli and Salmonella, Vol. 2, Ch. 114 (1996) 2047-2066, Neidhardt F C ed., ASM press, Washington, D.C.), as given in Table 2.







TABLE 2







Codon Usage in E. Coli.












Amino

Class
Amino

Class
















acid
Codon
I
II
III
acid
Codon
I
II
III



















Phe
TTT
55.0 9
29.08
67.14
Leu
CTT
9.7
5.56
19



TTC
44.91
70.92
32.86

CTC
10.4
8.03
9.04


 


Leu
TTA
10.99
3.44
20.09

CTA
3.09
0.83
6.81



TTG
13.02
5.47
15.05

CTG
52.79
76.67
29.99


 


Ser
TCT
13.26
32.41
19.63
Pro
CCT
13.71
11.23
28.3



TCC
15.02
26.56
11.34

CCC
11.19
1.63
16.26



TCA
10.83
4.79
22.09

CCA
18.63
15.25
31.5



TCG
16.88
7.39
10.6

CCG
56.47
71.89
23.94


 


Tyr
TAT
54.42
35.23
69.6
His
CAT
56.8
29.77
61.69



TAC
45.58
64.77
30.4

CAC
43.2
70.23
38.31


 


Stop
TAA



Gln
CAA
33.4
18.65
37.06



TAG




CAG
66.6
81.35
62.94


 


Cys
TGT
40.9
38.85
55.71
Arg
CGT
38.99
64.25
26.05



TGC
59.1
61.15
44.29

CGC
42.23
32.97
21.94


 


Stop
TGA




CGA
5.52
1.07
12.8


 


Trp
TGG
100
100
100

CGG
8.97
0.8
13.62


 


Ile
ATT
51.2
33.49
47.57
Val
GTT
23.74
39.77
34.33



ATC
44.37
65.94
26.65

GTC
22.48
13.45
18.95



ATA
4.43
0.57
25.78

GTA
14.86
19.97
21.78


 


Met
ATG
100
100
100

GTG
38.92
26.81
24.94


 


Thr
ACT
14.85
29.08
26.83
Ala
GCT
14.52
27.54
22.86



ACC
46.83
53.6
24.45

GCC
27.62
16.14
23.67



ACA
10.52
4.67
27.93

GCA
19.63
24.01
31.27



ACG
27.81
12.65
20.8

GCG
38.23
32.3
22.19


 


Asn
AAT
40.87
17.25
64.06
Asp
GAT
62.83
46.05
70.47



AAC
59.13
82.75
35.94

GAC
37.17
53.95
29.53


 


Lys
AAA
75.44
78.55
72.21
Glu
GAA
68.33
75.35
66.25



AAG
24.56
21.45
27.79

GAG
31.67
24.65
33.75


 


Ser
AGT
13.96
4.52
18.73
Gly
GGT
32.91
50.84
31.79



AGC
30.04
24.33
17.61

GGC
43.17
42.83
24.51


 


Arg
AGA
1.75
0.62
15.63

GGA
9.19
1.97
24.75



AGG
1.54
0.29
9.96

GGG
14.74
4.36
18.95









The genes which served as the basis for the data in Table 2 were clustered by using factorial correspondence analysis into three classes. Class I contains genes involved in most metabolic processes. Class II genes correspond to genes highly and continuously expressed during exponential growth. Class III genes are implicated in horizontal transfer of DNA. One can see that the distribution of codons in class III genes is more or less even, whereas it is extremely biased in class II genes (in particular, codons terminated in A are selected against).
The mutations on the codon level which were introduced in the T7 coding sequence are shown in Table 3.







TABLE 3







T7 Polymerase and Variants Thereof.












T7 enzyme/
WT
Mutated
SEQ


#
variant
codon
codon
ID NO:





 1
Wild-type

—
 1, 2


 


 2
Cys125Ser
TGC
AGC
 3, 4


 


 3
Cys347Ser
TGT
AGC
 5, 6


 


 4
Cys492Ser
TGC
AGC
 7, 8


 


 5
Cys515Ser
TGC
AGC
 9, 10


 


 6
Cys723Ser
TGC
AGC
11, 12


 


 7
Cys839Ser
TGT
AGC
13, 14


 


 8
Cys125Ser
TGC
AGC
15, 16



Cys347Ser
TGT
AGC




Cys492Ser
TGC
AGC




Cys515Ser
TGC
AGC




Cys723Ser
TGC
AGC




Cys839Ser
TGT
AGC



 9
Val426Leu
GTT
CTG
17, 18


 


10
Cys723Ser
TGC
AGC
19, 20



Val426Leu
GTT
CTG



 


11
Val426IIe
GTT
ATC
21, 22


 


12
Cys723Ser
TGC
AGC
23, 24



Val426Ile
GTT
ATC



 


13
Val426Phe
GTT
TTC
25, 26


 


14
Cys723Ser
TGC
AGC
27, 28



Val426Phe
GTT
TTC



 


15
Ser633Met
TCA
ATG
29, 30


 


16
Cys723Ser
TGC
AGC
31, 32



Ser633Met
TCA
ATG



 


17
Val650Leu
GTG
CTG
33, 34


 


18
Cys723Ser
TGC
AGC
35, 36



Val650Leu
GTG
CTG



 


19
Thr654Leu
ACC
CTG
37, 38


 


20
Cys723Ser
TGC
AGC
39, 40



Thr654Leu
ACC
CTG



 


21
Ala702Val
GCT
GTT
41, 42


 


22
Cys723Ser
TGC
AGC
43, 44



Ala702Val
GCT
GTT



 


23
Val795Ile
GTA
ATC
45, 46


 


24
Cys723Ser
TGC
AGC
47, 48



Val795Ile
GTA
ATC



 


25
Ala702Val
GCT
GTT
49, 50



Val795Ile
GTA
ATC



 


26
Cys723Ser
TGC
AGC
51, 52



Ala702Val
GCT
GTT




Val795Ile
GTA
ATC



 


27
Val426Leu
GTT
CTG
53, 54



Ala702Val
GCT
GTT



 


28
Cys723Ser
TGC
AGC
55, 56



Val426Leu
GTT
CTG




Ala702Val
GCT
GTT



 


29
Val426Leu
GTT
CTG
57, 58



Val795Ile
GTA
ATC



 


30
Cys723Ser
TGC
AGC
59, 60



Val426Leu
GTT
CTG




Val795Ile
GTA
ATC



 


31
Val426Leu
GTT
CTG
61, 62



Ala702Val
GCT
GTT




Val795Ile
GTA
ATC



 


32
Cys723Ser
TGC
AGC
63, 64



Val426Leu
GTT
CTG




Ala702Val
GCT
GTT




Val795Ile
GTA
ATC



 


33
Cys125Ser
TGC
AGC
65, 66



Cys347Ser
TGT
AGC




Cys492Ser
TGC
AGC




Cys515Ser
TGC
AGC




Cys723Ser
TGC
AGC




Cys839Ser
TGT
AGC




Val426Leu
GTT
CTG




Ala702Val
GCT
GTT




Val795Ile
GTA
ATC



 


34
Val426Leu
GTT
CTG
67, 68



Val650Leu
GTG
CTG




Ala702Val
GCT
GTT




Val795Ile
GTA
ATC



 


35
Cys723Ser
TGC
AGC
69, 70



Val426Leu
GTT
CTG




Val650Leu
GTG
CTG




Ala702Val
GCT
GTT




Val795Ile
GTA
ATC



 


36
Cys125Ser
TGC
AGC
71, 72



Cys347Ser
TGT
AGC




Cys492Ser
TGC
AGC




Cys515Ser
TGC
AGC




Cys723Ser
TGC
AGC




Cys839Ser
TGT
AGC




Val426Leu
GTT
CTG




Val650Leu
GTG
CTG




Ala702Val
GCT
GTT




Val795Ile
GTA
ATC









On the amino acid level, the T7 variants are shown in the even-numbered SEQ ID NOs: 4 to 72.
The nucleotide sequences encoding the mutated T7 polypeptides which were expressed in E. coli are shown in the uneven-numbered SEQ ID NOs: 3 to 71. The nucleotide sequences are represented including the start codons for N-terminal Methionine but without any other additional artificial N-terminal structures such as His-tags.
A His-tag (in the literature also referred to as a polyHis-tag) is an amino acid motif in proteins that typically consists of at least six consecutive His residues (His6). While the N-terminus of a T7 variant is preferred for the addition of the His-tag, the C-terminus of the polypeptide can serve as an alternative.
For clarification, a N-terminal His-tag can be located between the Methionine at the N-terminus of the respective variant T7 polypeptide and the subsequent amino acid according to the amino acid sequence of SEQ ID NO:2, i.e. Asn. Alternatively, the His-tag can be appended to the N-terminal Methionine of the T7 variant. When appended at the C-terminus of the variant T7 polypeptide the His-tag forms the C-terminal amino acids.
The T7 variants were modified further such that each polypeptide contained a His-tag at its N-terminus to facilitate purification.
Apart from the Histidines the His-tag can additionally comprise further amino acids depending on the design of the nucleotide sequence encoding the His-tag. Thus, an oligonucleotide linker with restriction sites typically adds 1 to 5 further amino acids to the nucleotide fragment encoding the consecutive His residues in the His-tag.
The amino acid sequences of the T7 variants of Tables 1a and 1b, and the nucleic acid sequences encoding the T7 variants are shown in the sequence listing of this disclosure. No His-tags are shown as these may differ sequence-wise, depending on the particular cloning vector used. However, the differences concerning the number of Histidines and the linker sequence, according to the preferred embodiments, are not expected to have a technical impact on the T7 variants according to the invention.
Example 2. Cloning of Nucleic Acids Encoding Variants of T7 RNA Polymerase
All molecular biological procedures were performed according to standard methods (Sambrook, J., Fritsch, E. F., Maniatis, T., Molecular cloning: A Laboratory Manual second Edition, B.27 (1989) Cold Spring Harbor Laboratory Press NY (USA)). Nucleotide sequences encoding the wild-type and the mutant T7 polypeptides were synthesized by a combinatorial synthesis strategy as described (van den Brulle, J., et al., Biotechniques 45 (3) (2008) 340-343).
For expression of each of the T7 variants, the respective coding DNA sequence was cloned in appropriate expression vectors in such a way that the mutated T7 coding sequence is inserted in the right orientation under the control of an appropriate promoter, preferably an inducible promoter, particularly preferably the lac-, lacUV5-, tac- or T5 promoter. Preferred expression vectors are pUC plasmids with lac- or lacUV5 promoters or pKK plasmids. For clarification an exemplary coding sequence comprises a DNA encoding a polypeptide selected from any of SEQ ID NOs: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, and 71, which optionally include a further modification such as a His-tag.
The synthesized genes were cloned in plasmid pUC18. The recipient strain for transformations was E. coli XL-1 blue. Transformed clones were grown at 37° C. in LB media containing ampicillin (100 μg/ml). Plasmids were isolated and digested using EcoRI and HindIII. The resulting fragments were subjected to agarose gel electrophoresis and the respective band corresponding to the variant T7 polymerase coding sequence was extracted. The isolated fragments were ligated into the expression plasmid pKKT5 (derived from pKK177-3 [Kopetzki, E., et al., Mol. Gen. Genet. 216 (1989) 149-155] by exchanging the tac-promotors with the T5-promoter derived from the plasmid pDS [Bujard, H., et al., Methods Enzymol. 155 (1987) 416-433]) which was digested with EcoRI and HindIII.
Plasmids were transformed into E. coli UT5600 (harboring plasmid pUBS520). Clones were grown at 37° C. in LB media containing ampicillin (100 μg/ml) and kanamycin (50 μg/ml).
Example 3. Expression of Variant T7 Polymerase Polypeptides
Transformed E. coli expression strains obtained as described in Example 2 were cultivated at 37° C. in LB media containing ampicillin (100 μg/ml) and kanamycin (50 μg/ml). Induction of recombinant expression was performed at an optical density of 0.7 (measured at 578 nm) by adding IPTG in a final concentration of 1 mM. After 5 hours the cells were harvested by centrifugation and frozen at −20° C.
Example 4. Purification of Variant T7 Polymerase Polypeptides
The following purification protocol is preferred according to the invention. His6-tagged wild-type T7 polypeptide and variants of T7 RNA polymerase were routinely purified to homogeneity using chromatographic methods. Reducing additives like 2-mercaptoethanol or DTT were omitted during the entire purification process. Frozen cells (typically 2.1 g) were suspended in 30 ml lysis buffer (50 mM Tris/HCl, pH 8.0 adjusted at room temperature, 0.2 M NaCl, 2 mM EDTA). After incubation at room temperature for 15 min, the cells were sonicated. After addition of 1 ml Polymin P cell debris was removed by centrifugation at 10,000 rpm for 10 min (Eppendorf centrifuge). The supernatant was dialyzed against Buffer A (20 mM potassium phosphate, pH 7.7, 1 mM EDTA, 50 mM NaCl, 5% glycerol). After centrifugation the pool was applied on a S-SepharoseTM ff column (1.6×10 cm) at a flow rate of 5 ml/min. Elution was performed using a NaCl gradient (0 M to 1 M in Buffer A). Fractions were monitored by running aliquots on a SDS gel. Fractions containing T7 RNA polymerase were pooled. After dialysis against Buffer B (50 mM Tris/HCl, pH 8.0 (pH adjusted at 25° C.), 1 M NaCl) each enzyme solution was applied on a Ni-chelating SepharoseTM ff column (4 ml). The column was washed using Buffer B. T7 RNA polymerase was eluted in Buffer B using an imidazole gradient of 0 M to 1 M. Fractions containing the enzyme were pooled. After dialysis against storage buffer (25 mM Tris/HCl, pH 7.5 [pH adjusted at 25° C.], 10 mM NaCl, 0.1 mM EDTA) pools were stored at −20° C.
Alternative purification protocol includes the use of reducing additives (less preferred): His6-tagged wild-type T7 polymerase and T7 variants were purified separately to homogeneity using metal chelate affinity matrix chromatography. Typically, wet frozen cells (2.1 g) were suspended in 30 ml Buffer C (50 mM Tris/HCl, pH 8.1 [pH adjusted at room temperature], 1 M NaCl). To the suspension 315 μl of a lysozyme solution (10 mg/ml) were added. After incubation at room temperature for 15 min, the cells were sonicated (6×2 min). The cell debris was removed by centrifugation at 5,000 rpm for 15 min. A fraction of the supernatant (25 ml) was applied onto a Ni-chelating Sepharose column (1 ml). The column was washed using a modified Buffer C which additionally contained 10 mM imidazole. His6-tagged polypeptides were eluted in a linear gradient (10 mM-500 mM imidazole in Buffer C). Enzyme-containing fractions were pooled. After dialysis against storage buffer (10 mM potassium phosphate, 200 mM KCl, 0.1 mM EDTA, 30 mM mercaptoethanol as a reducing additive, 50% glycerol, 0.1% Tween 20, pH 7.9) the pools were stored at −20° C.
Example 5. SDS Polyacrylamide Electrophoresis (SDS-PAGE)
Samples of T7 variants were prepared according to a procedure described in Example 4. T7 RNA polymerase and variants thereof were analzed by gel electrophoresis on polyacrylamide gels containing sodium dodecylsulphate (SDS). Gradient gels (NuPAGE, 4-12%, Bis-Tris Gel, Invitrogen) were used. Typically, protein samples (0.26 mg/ml, 18 μl) were mixed with 6 μl of NuPAGE LDS (Lithium dodecyl sulfate; LDS may also be substituted by sodium dodecyl sulfate) sample buffer, (4×, Invitrogen). After heating for 2 min at 85° C., samples (20 μl) were applied on the gel. The total amount of protein in a single lane of the gel was between 1 μg and 3 μg. Gels were run in SDS Running Buffer (1×MES, Invitrogen) at 200 V for 1 hour.
Protein bands in the gels were stained using the Simply Blue Safe Stain Kit (Invitrogen product number LT6060) according to the instructions of the manufacturer. A protein molecular weight marker (Mark 12, Invitrogen) was used to determine the apparent molecular weight and to identify monomeric and homopolymeric forms of T7 RNA polymerase and/or T7 variants.
As a reference sample, commercially available T7 RNA polymerase (without His-tag) was used (wild-type T7 commercially available from Roche Applied Science, Mannheim, Germany).
Example 6. Application of Conditions for Formation of Homodimers and Higher-Order Multimers
T7 enzyme and variants were purified according to Example 4 using the preferred procedure without a reducing agent. In order to compare tendencies to form intramolecular dimers and higher-order multimers, separate preparations of wild-type T7 polymerase (#1 in Table 3) and variants (##2 to 8 shown in Table 3) were incubated under conditions favoring the formation of homomultimers. To this end, samples of purified enzymes at a protein concentration of 0.2 mg/ml to 0.3 mg/ml were incubated individually at 37° C. for 16 hours in 25 mM Tris/HCl, pH 7.5 (pH adjusted at 25° C.), 0.1 mM EDTA, 100 mM NaCl under otherwise ambient conditions. This includes exposure to atmospheric oxygen.
Example 7. Analysis of Homodimer Formation
The capability to form dimers was studied for wild-type and T7 variants under stress conditions. To this end, samples were incubated in a buffer without reducing reagents. Protein monomers, dimers and higher-order multimers were determined by SDS gel electrophoresis as described in Example 5.
Samples of wild-type T7 RNA polymerase (0.2 to 0.3 mg/ml) were incubated at 37° C. for 16 hours in 25 mM Tris/HCl, pH 7.5 (adjusted at 25° C.), 0.1 mM EDTA, 100 mM NaCl. Aliquots were removed and applied on the SDS gels under reducing conditions (10 mM DTT added) or under non-reducing conditions (DTT omitted, no further reducing agent present). As shown in FIG. 1, the enzyme sample of wild-type T7 contained monomeric and dimeric forms following incubation under non-reducing conditions (in the present case without DTT, lane 1). Analysis of the sample under reducing conditions (with DTT) showed that the protein was completely transformed to the monomeric form (lane 2).
With reference to FIG. 1 (and in reference to Examples 5, 6, and 7), a stained SDS polyacrylamide gel is shown. The lanes designated M contain the Mark 12 size marker (Invitrogen). Lanes 1 and 2 contain wild-type T7 RNA polymerase. In both lanes the prominent band of fastest migrating protein represents monomeric T7 polypeptide. Samples of T7 RNA polymerase incubated for 16 h at 37° C. were treated or not treated with reducing reagents (DTT), and were subjected to electrophoresis. Lane 1: sample without DTT; Lane 2: sample treated with DTT. In lane 1 the regions marked with one and two asterisks indicate T7 multimers. The region marked with one asterisk contains only a faint smear. In the region marked with two asterisks, distinct bands can be discerned, indicating dimers and distinct higher-order homomultimers.
Further, samples of wild-type T7 and T7 variants (0.2 to 0.3 mg/ml each) were incubated at 37° C. for 16 hours in 25 mM Tris/HCl, pH 7.5 (adjusted at 25° C.), 0.1 mM EDTA, 100 mM NaCl. Aliquots were removed and applied on the SDS gels under reducing conditions or under non-reducing conditions. After incubation a sample of each treated preparation was subjected to SDS polyacrylamide gel electrophoresis as described in Example 5. Results are depicted in FIG. 2 (reducing reagents absent) and FIG. 3 (10 mM DTT added).
With reference to FIG. 2 (reducing reagents absent), and in reference to Examples 5, 6, and 7, a stained SDS polyacrylamide gel is shown. The lanes designated M contain the Mark 12 size marker (Invitrogen). No reducing agent was added prior to electrophoresis. Lane 1: wild-type T7 RNA polymerase without His-tag; Lane 2: wild-type T7 RNA polymerase including His6-tag; Lane 3: T7 variant #8 [Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, Cys723Ser, Cys839Ser] including His6-tag; Lane 4: T7 variant #6 [Cys723Ser] including His6-tag; Lane 5: T7 variant #3 [Cys347Ser] including His6-tag; Lane 6: T7 variant #7 [Cys839Ser] including His6-tag; Lane 7: T7 variant #2 [Cys125Ser] including His6-tag; Lane 8: T7 variant #4 [Cys492Ser] including His6-tag; Lane 9: T7 variant #5 [Cys515Ser] including His6-tag; To varying extents homodimers and higher-order homomultimers can be seen in lanes 1, 2, 5, 6, 7, 8, and 9. Lanes 3 and 4 are detectably free of homodimers and/or homomultimers.
With reference to FIG. 3 (10 mM DTT added), and in reference to Examples 5, 6, and 7, a stained SDS polyacrylamide gel is shown. The lanes designated M contain the Mark 12 size marker (Invitrogen). 10 mM DTT was added prior to electrophoresis, to provide reducing conditions. Lane 1: wild-type T7 RNA polymerase without His-tag; Lane 2: wild-type T7 RNA polymerase including His6-tag; Lane 3: T7 variant #8 [Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, Cys723Ser, Cys839Ser] including His6-tag; Lane 4: T7 variant #6 [Cys723Ser] including His6-tag; Lane 5: T7 variant #3 [Cys347Ser] including His6-tag; Lane 6: T7 variant #7 [Cys839Ser] including His6-tag; Lane 7: T7 variant #2 [Cys125Ser] including His6-tag; Lane 8: T7 variant #4 [Cys492Ser] including His6-tag; Lane 9: T7 variant #5 [Cys515Ser] including His6-tag.
Each lane with wild-type T7 or T7 variant in FIGS. 1, 2 and 3 represents an amount of 2.9 μg of protein.
The most surprising finding was that among the T7 variants with Cys-Ser substitutions tested, all those with a Cys723Ser mutation did not show detectable traces of homodimers or any higher-order homomultimers in SDS gels under the conditions specified in Example 5. This effect was not only observed in T7 variants with only Cys-Ser substitutions. The same effect was also obtained (i.e. homomultimers were detectably absent) when Cys723Ser was combined with any other substitution shown in Table 3. These results strongly suggest that the Cys723Ser mutation can advantageously be combined with other substitution mutations thus leading to variants with suppressed homomultimer formation.
It was noted that the effect of any other of the Cys-Ser substitution mutations selected from the group consisting of Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, and Cys839Ser was not comparable in that homodimers or any higher-order homomultimers were detectable in varying amounts. In SDS gels T7 variants with Cys839Ser just showed a detectable reduction of homomultimer formation but no absence of homomultimers.
As shown in FIG. 1, the Cys723Ser substitution alone is remarkably effective in suppressing homodimer (and homomultimer) formation. Nevertheless, accumulating more Cys-Ser substitutions in the T7 polypeptide is desirable, in order to minimize formation of heterodimers and -multimers, i.e. to suppress covalent disulfide bonding with other proteins but T7 polypeptide. In this regard, a T7 variant comprising Cys723Ser and one or more further substitutions selected from Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, and Cys839Ser has been found to be of great advantage.
Example 8. Analysis of DNA-Dependent RNA Polymerase Activity
A transcription-based non-radioactive assay (Method A) was used to measure the activity of purified wild-type and variants of T7 RNA polymerase obtained as described in Example 3. The enzyme activity was measured in 40 μl reaction buffer (40 mM Tris/HCl, 6 mM MgCl2, 1 mM NTP (each), 0.002% [v/v] polydocanol, 4 mM spermidine, pH 8.0, 1 μg of plasmid pSPT18 cleaved (i.e. linearized) with Sspl). T7 wild-type or a T7 variant polymerase enyzme was added in diluted form. After incubation at 37° C. for 30 min EDTA (0.4 M, 4 μl was added to stop the reaction.
Subsequently, each reaction mix (as an aliquot of 100 μl was mixed with 100 μl of SYBR Green II (diluted 1:4,000) and a volume of 1,890 μl 1×TE buffer were added. Fluorescence was measured photometrically (excitation wavelength: 485 nm, emission wavelength 530 nm) using a fluorimeter (Cary Eclipse, Varian). As a reference enzyme commercially available T7 RNA polymerase (Roche Applied Science, Roche Diagnostics GmbH, Mannheim) was used.
Alternatively (Method B), RNA quantification was done using Quant-iT RNA Assay (Invitrogen) on a LC480 Light Cycler platform (Roche Applied Science, Roche Diagnostics GmbH, Mannheim). As a reference enzyme commercially available T7 RNA polymerase (Roche Applied Science, Roche Diagnostics GmbH, Mannheim) was used.
To test the T7 enzyme and variants thereof under non-reducing conditions, comparative analysis was done in that in each case in a first experiment DTT was included, and in a second experiment DTT was omitted in the reaction mix.
Following incubation as described in Example 6, the enzymatic activity of samples containing protein multimers was tested, too.
Item A in Table 4 indicates the enzymatic activity of wild-type T7 polypeptide in the sample depicted in FIG. 1, lane 1 which shows the presence of dimers and higher-order multimers to a significant extent. Item B in the table corresponds to the protein in lane 2 of FIG. 1. As it becomes evident in the assay, enzymatic activity is lower in the absence of any reducing agent and increases upon addition of DTT. A comparable effect is obtained with other reducing agents with one or more thiol groups, such as mercaptoethanol or DTE.







TABLE 4







Activity of Wild-Type T7 RNA Polymerase Under Non-Reducing


andReducing Conditions.













fluorescence 




Assay setup
(arbitrary units)















A
no reducing agent
8.09



B
10 mM DTT in reaction mixture
12.43










The data show that the enzyme treated under non-reducing conditions shows a significantly reduced activity. This effect is directly correlated to the presence of protein dimers and higher-order multimers in the enzyme preparation.
Further, the effect of Cys-Ser substitutions in variant T7 polypeptides was determined; all assays were performed in the presence of 10 mM DTT. In each assay the concentration of the respective T7/T7 variant polymerase was 6.7 μg/ml. Table 5 shows exemplary data of wild-type and mutant T7 polypeptide enzymatic activities. T7 designations are made in accordance with those given in Table 3 above.







TABLE 5







Activity of Wild-Type T7 RNA Polymerase and Variant T7


Polypeptides.










T7 polypeptide
fluorescence (arbitrary units)







wild-type, # 1
46.4



T7 variant # 6
45.9



T7 variant # 8
49.2










Very surprisingly, no negative impact with regards to enzyme activity was observed even when six substitutions, i.e. Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, Cys723Ser, and Cys839Ser were accumulated in the same polypeptide (T7 variant #8, according to Table 3).
Example 9. Analysis of Thermostability: Half-Life Time
Further substitutions were made in the T7 polypeptide, in order to additionally enhance thermal stability of the polypeptide. T7 variants ##37 to 48 are shown in Table 6 below.
To determine the stability of wild-type T7 polymerase and T7 variants the half-life time was determined at 50° C. Samples of wild-type enzyme and purified variants (see Examples 3 and 4) were incubated in storage buffer (10 mM potassium phosphate, 200 mM KCl, 0.1 mM EDTA, 30 mM mercaptoethanol, 50% glycerol, 0.1% Tween 20, pH 7.9) at 50° C. At different time points (10, 20 and 30 min) samples were taken and the residual enzyme activity was measured as described in Example 3. The half-life time T1/2 expressed as a number of minutes [min] means that at this time point the activity of the respective T7 variant is 50% of the activity at the time point when the experiment was started, i.e. the exposure to 50° C. was applied. Table 6 summarizes results of the measurements.







TABLE 6







Half-Life Times at 50° C. of Wild-Type T7 RNA Polymerase and T7


Variants (Single Mutations and Combination Mutations).









#
T7 enzyme
T1/2 [min]












Reference









 1
Wild-type 
6.0-9.7









Single amino acid substitution









37
Val426Leu
 25.0


38
Val426Ile
 17.0


39
Ser633Met
 13.0


40
Val650Leu
 13.0


41
Thr654Leu
 13.0


42
Ala702Val
 22.0


43
Val795Ile
 29.0









Double amino acid substitution









44
Ala702Val
 22.0



Val795Ile



45
Val426Leu
 39.0



Ala702Va1



46
Va1426Leu
 40.0



Val795Ile










Triple amino acid substitution









47
Val426Leu
312.0



Ala702Val




Val795Ile










Quadruple amino acid substitution









48
Val426Leu
 64.0



Val650Leu




Ala702Val




Val795Ile









With regards to half-life times at 50° C., the inventors observed several surprising effects. Firstly, there were single amino acid exchanges without noticeable impact on thermostability, i.e. mutations which did not cause a substantial difference compared to the wild-type reference (#1). In this first group all T7 variants with a T1/2 value between 5 and 12 (including 5 and 12) were combined (not shown). A second group of T7 variants (not shown) was found in which the mutants had even shorter half-life times at 50° C., compared to the wild-type reference. Additionally, mutants which had lost enzymatic activity completely were combined in the second group. A third group of amino acid exchange mutations was found to enhance half-life time at 50° C. over the values found for the wild-type reference. A value greater than 12 was considered as indicating a substantial increase of thermostability in the respective T7 variant. The third group comprises the mutations according to ##37 to 48 as shown in Table 6.
Surprisingly, some amino acid substitutions which, according to theoretical predictions, were predicted to have a desired positive effect on thermostability did not lead to the expected results.
Very surprisingly, the amino acid substitutions shown in Table 6 could be combined with any of the Cys-Ser substitutions six substitutions described above, i.e. with Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, Cys723Ser, and Cys839Ser, wherein variant T7 polypeptides with DNA-dependent RNA activity were obtained. Even more surprising, T7 variants combining (a) either Cys723Ser or all of the above six Cys-Ser substitutions with (b) a single, a double, a triple, or a quadruple amino acid substitution as shown in Table 6 were found to be more thermostable than the wild-type T7 polypeptide. Combining thermostability with a reduced tendency to form intramolecular disulfide bridges, the T7 variants ##10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 33, 35, and 36 (according to Table 3) are particularly advantageous and very much preferred.
Example 10. Determination of Protein Concentration in Solutions
Protein concentrations were determined by measuring the optical density at 280 nm using a molar extinction coefficient of E280 nm=1.4×105 M−1 cm−1 as described (He, B., et al., Protein Expr Purif 9 (1997) 142-151).
All publications, patents and applications are hereby incorporated by reference in their entirety to the same extent as if each such reference was specifically and individually indicated to be incorporated by reference in its entirety.
While this disclosure has been described as having an exemplary design, the present disclosure may be further modified within the spirit and scope of this disclosure. This application is therefore intended to cover any variations, uses, or adaptations of the disclosure using its general principles. Further, this application is intended to cover such departures from the present disclosure as come within the known or customary practice in the art to which this disclosure pertains.

## Claims

1. An aqueous solution being devoid of a reducing agent with a thiol group, the aqueous solution comprising:
a variant polypeptide of T7 RNA polymerase, the variant having DNA-dependent RNA polymerase activity and comprising the amino acid sequence of SEQ ID NO.:2, including a Cysteine residue at amino acid position between 510 and 530, numbered from the N-terminus of SEQ ID NO.:2, further having a Serine residue substitution for the Cysteine residue at amino acid position 723, numbered from the N-terminus of SEQ ID NO.:2, wherein in the aqueous solution the variant is devoid of homomultimer formation of intermolecular disulfide bond(s).

2. The aqueous solution according to claim 1, wherein the variant comprises a Cysteine-Serine substitution selected from the group consisting of Cys125Ser, Cys347Ser, Cys492Ser, Cys515Ser, and Cys839Ser.

3. The aqueous solution according to claim 1, wherein the variant further comprises an N-terminal His-tag.

4. The aqueous solution according to claim 1, wherein the variant further comprises an N-terminal Methionine.

5. The aqueous solution according to claim 1, wherein the reducing agent with the thiol group is selected from the group consisting of mercaptoethanol, dithiothreitol, dithioerythritol.