# Patent

## Title
Expression system

## Abstract

A perfect palindrome operator sequence-based protein expression system is provided. The expression system comprises a promoter; and a perfect palindrome operator sequence, wherein the promoter is not T7. The expression system is preferably employed for the production of recombinant proteins by fermentation.

## Background
The present invention concerns an expression system suitable for the microbial expression of recombinant polypeptides.
T7-based perfect palindrome operator sequence-based protein expression systems are known from U.S. Pat. No. 6,537,779. T7 based systems suffer from drawbacks in that operation of the T7 system requires phage polymerase which is commonly provided by inserting a λDE3 prophage expressing the required phage polymerase into the Escherichia coli host strain to create lysogenic host strains. The phage polymerase can also be delivered to the cell by infection with a specialised λ transducing phage that carries the gene for the phage polymerase (e.g. T7 RNA polymerase). The λDE3 prophage lacks the genetic elements required for the excision of the prophage to form lytic phage particles. However, λDE3 lysogenic host strains have been shown to release phage particles and thus cause undesirable infections in fermentation plants. Indeed, the use of λDE3 strains is not permitted by certain fermentation plant operators.
Expression of the heterologous protein prior to induction is not desirable because some heterologous proteins have deleterious effects on the host cell growth and plasmid stability which reduce overall productivity. To avoid this, T7-based expression systems generally control expression of heterologous proteins at two levels. First, induction of expression of the T7 RNA polymerase gene to produce T7 RNA polymerase is required to drive expression from the T7 promoter. Secondly, the T7 promoter itself also needs to be induced. This increases the complexity of operating T7-based expression systems.
There are a large number of heterologous protein expression systems with different modes of control and induction, making selection and optimisation of the expression system/fermentation process for proteins of interest a largely empirical process. This is time consuming and undesirable. Thus, there is a need for systems which can provide improved control of expression and improved levels of protein expression without the use of phage polymerase and lysogenic host strains. There is also a need for systems which can provide inducible heterologous expression in prokaryotic cells, as well as eukaryotic cells such as mammalian and yeast cells.
According to the present invention, there is provided a perfect palindrome operator sequence-based protein expression system comprising:
a) a promoter; and
b) a perfect palindrome operator sequence;
characterised in that the promoter is not T7.
Promoters which can be employed in the expression system of the present invention are commonly host RNA polymerase-based promoter systems, and preferably E. coli RNA polymerase-based promoter systems. Examples of promoters which can be employed include T7A1, T7A2, T7A3, λpL, λpR, lac, lacUV5, trp, tac, trc, phoA and rrnB.
Operator sequences which may be employed in the expression system according to the present invention include lac, gal, deo and gln. One or more perfect palindrome operator sequences may be employed. In many preferred embodiments, two perfect palindrome operator sequences are employed, most advantageously one operator sequence being located downstream of the promoter, and one operator sequence being located upstream of the promoter. When two operator systems are employed, the operator sequences are preferably spaced to maximise control of the promoter. In many embodiments, the spacing is from 85 to 150 base pairs apart, preferably from 90 to 126 base pairs apart, and most preferably 91 or 92 base pairs apart. In certain embodiments, an operator sequence overlaps with the transcriptional start point
It will be recognised that the operator system is commonly employed with an appropriate repressor sequence. Repressor sequences produce repressor protein, for example lad gene sequence when using the lac operators. Other lac repressor sequences may also be used, for example the lacIQ sequence can be used to increase the level of lac repressor protein. The repressor sequence may also be provided by the host cell genome or by using an additional compatible plasmid.
The expression system may be integrated into the host cell genome, but is preferably comprised within an extrachromosomal element such as a plasmid. Alternatively, the expression system may be incorporated into phage or viral vectors and these used to deliver the expression system into the host cell system. Plasmids or expression vectors can be assembled by methods known in the art. The plasmid typically also comprises one or more of the following: a selectable marker, for example a sequence conferring antibiotic resistance, a cer stability sequence and an expression cassette. The expression system may also incorporate a signal sequence if secretion of the desired protein is required.
Expression may be induced by the addition of an inducer such as isopropyl-β-D-1-thiogalactopyranoside (IPTG), analogues of IPTG such as isobutyl-C-galactoside (IBCG), lactose or melibiose. Other inducers may be used and are described more fully elsewhere (e.g. see The Operon, eds Miller and Renznikoff (1978)). Inducers may be used individually or in combination. The construction of appropriate plasmids or expression vectors will be apparent to the scientist of ordinary skill.
The expression system of the present invention can be employed to express proteins in host cells, and especially in microorganisms. As used herein, “proteins” refers generally to peptides and proteins having more than about 10 amino acids. The host cell may be prokaryotic or eukaryotic. Examples of prokaryotic cells include bacterial cells, for example gram-negative bacterial cells, including E. coli, Salmonella typhimurium, Serratia marsescens and Pseudomonas aeruginosa, and gram-positive bacterial cells including Bacillus subtilis. Examples of eukaryotic cells include yeasts, such as Pichia pastoris, Saccharomyces cerevisiae, Hansenula polymorpha, Kluyveromyces lactis, Schizosaccharomyces pombe. Mammalian host cells which can be employed include human cell lines, such as human embryonic kidney and PERC.6 cells; murine cell lines, such as NS0 cells; and particularly hamster cell lines such as baby hamster kidney cells and especially Chinese hamster ovary cells. Other eukaryotic host cells such as those of filamentous fungi, plant, insect, amphibian cells or ovarian species may also be employed. Preferred host cells are bacteria, particularly enterobacteriacae, preferably E. coli, and especially B or K12 strains thereof.
The expression system of the present invention is commonly employed in the form of a plasmid, and plasmids comprising a promoter and a perfect palindrome operator sequence, wherein the promoter is not T7, form another aspect of the present invention. The plasmids may be autonomously replicating plasmids or integrative plasmids.
The expression system of the present invention is advantageously employed for the manufacture of proteins, especially recombinant proteins, by culturing recombinant cells. For the expression of proteins, it will be recognised that the promoter and operator sequence are operably linked to DNA encoding a protein to be expressed.
Accordingly, the present invention also provides a method for the production of a protein which comprises expressing an expression system comprising
a) a promoter;
b) a perfect palindrome operator sequence; and
c) an expression cassette for a protein;
characterised in that the promoter is not T7.
One or more promoters, operator sequences and expression cassettes, which may be the same or different, may be present if desired.
The expression system is expressed by methods well known in the art for the cells employed. Preferred expression methods include culturing the recombinant cells in growth medium, especially by fermentation, and then recovering the expressed protein. The term “growth medium” refers to a nutrient medium used for growing the recombinant cells. In many embodiments, a nutrient solution is employed. Suitable growth media for given recombinant cells are well known in the art.
The present invention is illustrated without limitation by the following examples.



BRIEF DESCRIPTION OF THE DRAWINGS
The accompanying drawings, which are included to provide a further understanding of the invention and are incorporated in and constitute a part of this application, illustrate embodiment(s) of the invention and together with the description serve to explain the principle of the invention. In the drawings:
FIG. 1 is a D1.3 Fab expression cassette according to an embodiment of the present invention;
FIG. 2 shows the result of the accumulation level of hTNFa according to Example 7;
FIG. 3 shows Western blot analysis for strain CLD038 according to Example 9;
FIG. 4 shows the hTNFa productivity profile for Strain CLD030 according to Example 11;
FIG. 5 shows the DNA sequence for a synthetic bispecific single chain tetravalent diabody (bsctDb) that was designedaccording to Example 15;
FIG. 6 shows SEQ ID NO: 23 according to Example 16;
FIG. 7 shows SEQ ID NO: 24 according to Example 16;
FIG. 8 shows SEQ ID NO: 25 according to Example 16;
FIG. 9 shows SEQ ID NO: 26 according to Example 17;
FIG. 10 shows the expression and accumulation of HadL protein according to Example 17;
FIG. 11 shows the growth of CLD075 and expression/accumulation of HadL protein following induction according to Example 18;
FIG. 12 shows SEQ ID NO: 33 according to Example 21;
FIG. 13 shows SEQ ID NO: 34 according to Example 21;
FIG. 14 shows the expression and secretion into the growth medium by the CHO cells of IgG Fc protein according to Example 21;
FIG. 15 shows SEQ ID NO: 35 according to Example 20;
FIG. 16 shows SEQ ID NO: 36 according to Example 20;
FIG. 17 shows the accumulation level of hTNF; and
FIG. 18 shows a plasmid map for pAVE013 according to an embodiment of the present invention.
1. Generation of pAVE Series of Vectors
Vectors pAVE011, pAVE012 and pAVE013
The starting vector for the generation of pAVE011 was pZT7#2.0, prepared as described in U.S. Pat. No. 6,537,779. pZT7#2.0 has a pAT153 vector backbone, cer stability sequence, tet A/R, a single native lac operator sequence upstream of the gene of interest and an upstream T4 transcription terminator. A T7A3 promoter and dual perfect palindrome lac operators were cloned into this plasmid using synthetic oligonucleotide linkers by means of the Nco I, EcoR I and Xba I restriction enzyme sites.
Linker 12.1 was prepared by annealing the oligonucleotides 1 and 2.1:







(SEQ ID NO 1)


Oligonucieotide 1


5′CATGTGGGAATTGTGAGCGCTCACAATTCCAAGAACAATCCTGCACG


 


(SEQ ID NO 2)


Oligonucleotide 2.1


5′AATTCGTGCAGGATTGTTCTTGGAATTGTGAGCGCTCACAATTCCCA






The linker was then ligated to plasmid pZT7#2.0 and transformed into cloning host strain XL-1 Blue MR (Stratagene) as an Nco I/EcoR I fragment. Initial screening of transformants was by restriction digestion using Nco I. The sequence was confirmed by sequencing. The resultant plasmid was named pAVE012.
The T7A3 promoter cassette was then cloned into pAVE012 by annealing oligonucleotides 3 and 4:







(SEQ ID NO 3)


Oligonucleotide 3


5′AATTCAAACAAAACGGTTGACAACATGAAGTAAACACGGTACGATGTA


 


CCGGAATTGTGAGCGCTCACAATTCCCCA


 


(SEQ ID NO 4)


Oligonucleotide 4


5′CTGGTGGGGGGTTGTGGGCGCTCGCGGTTCCGGTGCGTCGTGCCGT


 


GTTTGCTTCGTGTTGTCGGCCGTTTTGTTTG






the annealed oligonucleotides being ligated to plasmid pAVE012 and transformed into cloning host strain XL-1 Blue MR (Stratagene) as an Xba I/EcoR I fragment. Initial screening was by restriction digest of plasmid DNA. The sequence was then confirmed by sequencing. The resultant plasmid was named pAVE011.

Human TNFα gene was cloned into this plasmid as an Nde I/Xho I fragment to generate pAVE013. A plasmid map for pAVE013 is presented in FIG. 18. This shows the arrangement of operators and promoter, and the restriction enzyme sites used in the construction. The operators are both perfect palindrome lac operators. RBS is the ribosomal binding site. The vector includes a pAT153 vector backbone, a cer stability sequence, an inducible tetracycline resistance gene (tet A/R), and an upstream T4 transcription terminator.
Vectors pAVE038 and pAVE041
The starting vector for the generation of pAVE038 was pZT7#2.0, prepared as described in U.S. Pat. No. 6,537,779. A tac promoter and single native lac operator were cloned into this plasmid using a synthetic oligonucleotide linker by means of the EcoR I and Xba I restriction enzyme sites.
Linker 1112 was made by annealing the oligonucleotides 11 and 12







(SEQ ID NO 5)


Oligonucleotide 11 


5′AATTTTCTGAAATGAGCTGTTGACAATTAATCATCGGCTCGGATACTG


 


TGTGGAATTGTGAGCGGATAACAATTCCCCA


 


(SEQ ID NO 6)


Oligonucleotide 12 


5′CTAGTGGGGAATTGTTATCCGCTCACAATTCCACACAGTATCCGAGCC


 


GATGATTAATTGTCAACAGCTCATTTCAGAA






The linker was then ligated to plasmid pZT7#2.0 and transformed into cloning host strain XL-1 Blue MR (Stratagene) as an Xba I/EcoR I fragment. Initial screening of transformants was by restriction digestion using Nco I. The sequence was confirmed by sequencing. The resultant plasmid was named pAVE038.
A human TNFα gene was cloned into this plasmid as an Nde I/Xho I fragment to generate plasmid pAVE041.
Vector pAVE037 and pAVE040
The starting vector for the generation of pAVE037 was pZT7#2.0 prepared as described in U.S. Pat. No. 6,537,779. A tac promoter and single perfect palindrome lac operator were cloned into this plasmid using a synthetic oligonucleotide linker by means of the EcoR I and Xba I restriction enzyme sites.
Linker 1314 was made by annealing the oligonucleotides 13 and 14







(SEQ ID NO 7)


Oligonucleotide 13 


5′AATTTTCTGAAATGAGCTGTTGACAATTAATCATCGGCTCGGATACTG


 


TGTGGAATTGTGAGCGCTCACAATTCCCCA


 


(SEQ ID NO 8)


Oligonucleotide 14 


5′CTAGTGGGGAATTGTGAGCGCTCACAATTCCACACAGTATCCGAGCCG


 


ATGATTAATTGTCAACAGCTCATTTCAGAA






The linker was then ligated to plasmid pZT7#2.0 and transformed into cloning host strain XL-1 Blue MR (Stratagene) as an Xba I/EcoR I fragment. Initial screening of transformants was by restriction digestion using Nco I. The sequence was confirmed by sequencing. The resultant plasmid was named pAVE037.
A human TNFα gene was cloned into this plasmid as an Nde I/Xho I fragment to generate pAVE040.
Vector pAVE028 and pAVE030
The starting vector for the generation of pAVE028 was pAVE012. A T7A3 promoter cassette was cloned into pAVE012 by annealing oligonucleotides 5 and 6.







(SEQ ID NO 9)


Oligonucleotide 5 


5′AATTCGAAACAAAACGGTTGACAACATGAAGTAAACACGGTACGATGT


 


ACCGGAATTGTGAGCGCTCACAATTCCCCA


 


(SEQ ID NO 10)


Oligonucleotide 6 


5′CTGGTGGGGGGTTGTGGGCGCTCGCGGTTCCGGTGCGTCGTGCCGTG


 


TTTGCTTCGTGTTGTCGGCCGTTTTGTTTCG






the annealed oligonucleotides being ligated to plasmid pAVE012 and transformed into cloning host strain XL-1 Blue MR (Stratagene) as an Xba I/EcoR I fragment. Initial screening was by restriction digest of plasmid DNA. The sequence was then confirmed by sequencing. The resultant plasmid was named pAVE028.

A human TNFα gene was cloned into this plasmid as an Nde I/Xho I fragment to generate pAVE030.
Vector pAVE007 and pAVE031
The starting vector for the generation of pAVE007 was pZT7#2.0 prepared as described in U.S. Pat. No. 6,537,779. A T7A3 promoter and single perfect palindrome lac operator was cloned into this plasmid using a synthetic oligonucleotide linker by means of the EcoR I and Xba I restriction enzyme sites.
The linker containing the T7A3 promoter was made up of oligonucleotides 3 and 4.







(SEQ ID NO 3)


Oligonucleotide 3 


5′AATTCAAACAAAACGGTTGACAACATGAAGTAAACACGGTACGATGTA


 


CCGGAATTGTGAGCGCTCACAATTCCCCA


 


(SEQ ID NO 4)


Oligonucleotide 4 


5′CTGGTGGGGGGTTGTGGGCGCTCGCGGTTCCGGTGCGTCGTGCCGTGT


 


TTGCTTCGTGTTGTCGGCCGTTTTGTTTG






Oligonucleotides 3 and 4 were annealed, the linker formed was then ligated to plasmid pZT7#2.0 and transformed into cloning host strain XL-1 Blue MR (Stratagene) as an Xba I/EcoR I fragment. Initial screening was by restriction digest of plasmid DNA. The sequence was then confirmed by sequencing. The resultant plasmid was named pAVE007.
A human TNFα gene was cloned into this plasmid as an Nde I/Xho I fragment to generate pAVE031.
Vectors pAVE029 and pAVE027
The starting vector for the generation of pAVE029 was pZT7#2.0 prepared as described fully in U.S. Pat. No. 6,537,779. A λpL promoter and single perfect palindrome lac operator was cloned into this plasmid using synthetic oligonucleotide linker by means of the EcoR I and Xba I restriction enzyme sites.
Linker 78 was made by annealing the oligonucleotides 7 and 8







(SEQ ID NO 11)


Oligonuciectide 7 


5′AATTATCTCTGGCGGTGTTGACATAAATACCACTGGCGGTGATACTGA


 


GCGGAATTGTGAGCGCTCACAATTCCCCA


 


(SEQ ID NO 12)


Oligonucleotide 8 


5′CTAGTGGGGAATTGTGAGCGCTCACAATTCCGCTCAGTATCACCGCCA


 


GTGGTATTTATGTCAACACCGCCAGAGAT






The linker was then ligated to plasmid pZT7#2.0 and transformed into cloning host strain XL-1 Blue MR (Stratagene) as an Xba I/EcoR I fragment. Initial screening of transformants was by restriction digestion using Nco I. The sequence was confirmed by sequencing. The resultant plasmid was named pAVE029.
A human TNFα gene was cloned into this plasmid as an Nde I/Xho I fragment to generate pAVE027.
Vectors pAVE043 and pAVE044
The starting vector for the generation of pAVE043 was pAVE012. A tac promoter cassette was cloned into pAVE012 by annealing oligonucleotides 17 and 18:







(SEQ ID NO 37)


Oligonucleotide 17 


5′AATTTTCTGAAATGAGCTGTTGACAATTAATCATCGGCTCGTATAATG


 


TGTGGAATTGTGAGCGCTCACAATTCCCCA


 


(SEQ ID NO 38)


Oligonucleotide 18 


5′CTAGTGGGGAATTGTGAGCGCTCACAATTCCACACATTATACGAGCCG


 


ATGATTAATTGTCAACAGCTCATTTCAGAA






the annealed oligonucleotides being ligated to plasmid pAVE012 and transformed into cloning host strain XL-1 Blue MR (Stratagene) as an Xba I/EcoR I fragment. Initial screening was by restriction digest of plasmid DNA. The sequence was then confirmed by sequencing. The resultant plasmid was named pAVE043.

A human TNFα gene was cloned into this plasmid as an Nde I/Xho I fragment to generate pAVE044.
Vectors pAVE034 and pAVE035
The starting vector for the generation of pAVE034 was pAVE012. A λpL promoter cassette was cloned into pAVE012 by annealing oligonucleotides 9 and 10:







(SEQ ID NO 39)


Oligonucleotide 9 


5′AATTCATCTCTGGCGGTGTTGACATAAATACCACTGGCGGTGATACTG


 


AGCGGAATTGTGAGCGCTCACAATTCCCCA


 


(SEQ ID NO 40)


Oligonucleotide 10 


5′CTAGTGGGGAATTGTGAGCGCTCACAATTCCGCTCAGTATCACCGCCA


 


GTGGTATTTATGTCAACACCGCCAGAGATG






the annealed oligonucleotides being ligated to plasmid pAVE012 and transformed into cloning host strain XL-1 Blue MR (Stratagene) as an Xba I/EcoR I fragment. Initial screening was by restriction digest of plasmid DNA. The sequence was then confirmed by sequencing. The resultant plasmid was named pAVE034.

A human TNFα gene was cloned into this plasmid as an Nde I/Xho I fragment to generate pAVE035.
Vector pAVE020 and pAVE021
The starting vector for the generation of pAVE020 was pAVE012. A λpL promoter cassette was cloned into pAVE012 by annealing oligonucleotides 7 and 8.







(SEQ ID NO 11)


Oligonucleotide 7 


5′AATTATCTCTGGCGGTGTTGACATAAATACCACTGGCGGTGATACTGA


 


GCGGAATTGTGAGCGCTCACAATTCCCCA


 


(SEQ ID NO 12)


Oligonucleotide 8 


5′CTAGTGGGGAATTGTGAGCGCTCACAATTCCGCTCAGTATCACCGCCA


 


GTGGTATTTATGTCAACACCGCCAGAGAT






the annealed oligonucleotides being ligated to plasmid pAVE012 and transformed into cloning host strain XL-1 Blue MR (Stratagene) as an Xba I/EcoR I fragment. Initial screening was by restriction digest of plasmid DNA. The sequence was then confirmed by sequencing. The resultant plasmid was named pAVE020.

A human TNFα gene was cloned into this plasmid as an Nde I/Xho I fragment to generate pAVE021.
Vectors pAVE016 and pAVE017
The starting vector for the generation of pAVE016 was pAVE012. A tac promoter cassette was cloned into pAVE012 by annealing oligonucleotides 15 and 16.







(SEQ ID NO 13)


Oligonucleotide 15 


5′AATTCCTGAAATGAGCTGTTGACAATTAATCATCGGCTCGTATAATGT


 


GTGGAATTGTGAGCGCTCACAATTCCCCA


 


(SEQ ID NO 14)


Oligonucieotide 16 


5′CTAGTGGGGAATTGTGAGCGCTCACAATTCCACACATTATACGAGCCG


 


ATGATTAATTGTCAACAGCTCATTTCAGG






the annealed oligonucleotides being ligated to plasmid pAVE012 and transformed into cloning host strain XL-1 Blue MR (Stratagene) as an Xba I/EcoR I fragment. Initial screening was by restriction digest of plasmid DNA. The sequence was then confirmed by sequencing. The resultant plasmid was named pAVE016.

A human TNFα gene was cloned into this plasmid as an Nde I/Xho I fragment to generate pAVE017.
Vector pAVE049
The starting vector for the generation of pAVE049 was pAVE017. The tac promoter cassette was not altered. To increase the spacing between the two operators from 91 to 124 base pairs, an EcoR I linker was cloned in. This was made up of oligonucleotides 19 and 20.







(SEQ ID NO 15)


Oligonucleotide 19 


5′AATTCACCGGTGTACAGTCATGTACAACCGGTG


 


(SEQ ID NO 16)


Oligonucleotide 20 


5′AATTCACCGGTTGTACATGACTGTACACCGGTG






Initial screening was by restriction digest of plasmid DNA. The sequence was then confirmed by sequencing. The resultant plasmid was named pAVE049.
Vector pAVE046
The starting vector for the generation of secretion vector pAVE046 was pAVE027. A D1.3 Fab expression cassette (FIG. 1, SEQ ID NO 17) was cloned as an Nde I-Bam HI fragment. Initial screening was by restriction digest of plasmid DNA. The sequence was then confirmed by sequencing. The resultant plasmid was named pAVE046.







TABLE 1







Summary of pAVE vectors










Plasmid
Promoter
Operator System
Comments





pAVE041
tac
Single native lac sequence



pAVE017
tac
Double perfect palindrome
Operator spacing 91




sequences (DPPS)
base pairs





(DPPS91)


pAVE040
tac
Single perfect palindrome




sequence (SPPS)


pAVE049
tac
Double perfect palindrome
Operator spacing




sequences
124 base pairs





(DPPS124)


pAVE013
T7A3
Double perfect palindrome
Operator spacing 91




sequences
base pairs





(DPPS91)


pAVE030
T7A3
Double perfect palindrome
Operator spacing 92




sequences
base pairs





(DPPS92)


pAVE031
T7A3
Single perfect palindrome




sequence


pAVE021
λpL
Double perfect palindrome
Operator spacing 91




sequences
base pairs





(DPPS91)


pAVE035
λpL
Double perfect palindrome
Operator spacing 92




sequences
base pairs





(DPPS92)


pAVE027
λpL
Single perfect palindrome




sequence


pAVE046
λpL
Single perfect palindrome
Secretion Vector




sequence









2. Generation of Recombinant Strains

E. coli strains W3110 (available from the American Type Culture Collection as strain ATCC27325) and BL21 (available from EMD Biosciences Inc, San Diego, USA) were transformed by electroporation with the plasmids as described in Table 2 below. The resultant recombinant strains were purified and maintained in glycerol stocks at −80° C.







TABLE 2







Recombinant strains constructed












Description





(protein:promoter:operator
Recombinant


Host
Plasmid
system)
Designation No





ATCC27325
pAVE013
TNFα:T7A3:DPPS91
CLD018


ATCC27325
pAVE030
TNFα:T7A3:DPPS92
CLD026


ATCC27325
pAVE031
TNFα:T7A3:SPPS
CLD032


ATCC27325
pAVE041
TNFα:tac:single native lacO
CLD043


ATCC27325
pAVE017
TNFα:tac:DPPS91
CLD019


ATCC27325
pAVE040
TNFα:tac:SPPS
CLD042


ATCC27325
pAVE049
TNFα:tac:DPPS124
CLD050


ATCC27325
pAVE021
TNFα:λpL:DPPS91
CLD021


ATCC27325
pAVE035
TNFα:λpL:DPPS92
CLD038


ATCC27325
pAVE027
TNFα:λpL:SPPS
CLD030


BL21
pAVE013
TNFα:T7A3:DPPS91
CLD035


BL21
pAVE030
TNFα:T7A3:DPPS92
CLD028


ATCC27325
pAVE046
D1.3 Fab:λpL:SPPS
CLD048









Comparison 1

The starting vector for the generation of a plasmid with the T7A3 promoter without any operator was pZT7#2.0. A T7A3 promoter was cloned into this plasmid using synthetic oligonucleotide linker by means of the EcoR I and Xba I restriction enzyme sites.
Linker 2122 was made by annealing the oligonucleotides 21 and 22







(SEQ ID NO 18)


Oligonucleotide 21 


5′AATTCGAAACAAAACGGTTGACAACATGAAGTAAACACGGTACGATGT


 


ACCACATGAAACGACAGTGAGTCA


 


(SEQ ID NO 19)


Oligonucleotide 22 


5′CTAGTGACTCACTGTCGTTTCATGTGGTACCTCGTACCGTGTTTACTT


 


CATGTTGTCAACCGTTTTGTTTCG






The linker was then ligated to plasmid pZT7#2.0 and transformed into cloning host strain XL-1 Blue MR (Stratagene) as an Xba I/EcoR I fragment. Initial screening was by restriction digest of plasmid DNA. The sequence was then confirmed by sequencing. Eighty-two clones were screened by restriction digest and sequencing.
No clones were identified with the correct T7A3 promoter sequence (all contained mutations in the sequence). This suggests that construction of plasmids containing this powerful constitutive promoter is problematic.
Comparison 2
The starting vector for the generation of a plasmid with the T7A3 promoter under the control of a single native Lac operator sequence was pZT7#2.0. A T7A3 promoter and native Lac operator (LacO) sequence was cloned into this plasmid using synthetic oligonucleotide linker by means of the EcoR I and Xba I restriction enzyme sites.
Linker 2324 was made by annealing the oligonucleotides 23 and 24







(SEQ ID NO 20)


Oligonucleotide 23 


5′AATTCGAAACAAAACGGTTGACAACATGAAGTAAACACGGTACGATGT


 


ACCGGAATTGTGAGCGGATAACAATTCCCCA


 


(SEQ ID NO 21)


Oligonucleotide 24 


5′CTAGTGGGGAATTGTTATCCGCTCACAATTCCGGTACATCGTACCGTG


 


TTTACTTCATGTTGTCAACCGTTTTGTTTCG






The linker was then ligated to plasmid pZT7#2.0 and transformed into cloning host strain XL-1 Blue MR (Stratagene) as an Xba I/EcoR I fragment. Initial screening was by restriction digest of plasmid DNA. The sequence was then confirmed by sequencing. Ninety-four clones were screened by restriction digestion and sequencing. Again no clones were identified with the correct sequence. However, one clone was found to have a near intact sequence. This clone contained an additional ‘G’ in the sequence approximately at position −37. It is difficult to assign exact position of the mutation since the expected sequence contains -GG- in this region. Human TNFα gene was cloned into the plasmid with the near intact sequence as an Nde I/Xho I fragment. Twenty colonies from the cloning host strain XL-Blue MR (Stratagene) were screened. One was positive clone with no mutations (other than the additional ‘G’ described above). This plasmid was transformed into a production host (ATCC27325) and the plasmid re-sequenced.
This indicated that the plasmid contained gross mutations in both the T7A3 promoter and the human TNFα sequences indicating that the use of the T7A3 promoter, even under the control of the native lac operator sequence, results in plasmid instability.



EXAMPLE 3
A vial of CLD032 was removed from the −80° C. freezer and allowed to thaw. 10 μl of the thawed glycerol stock was inoculated into 5 ml Luria Broth (LB, 5 g/L yeast extract (Oxoid), 10 g/L tryptone (Oxoid), and 5 g/L sodium chloride) supplemented with tetracycline (10 μg/ml) and glucose (1 g/L). This was incubated at 37° C. in an orbital shaker for 16 h. 500 μl of this culture was then used to inoculate two 250 ml Erlenmeyer flasks containing 50 ml of Luria Broth (composition as described above). The flasks were incubated at 37° C., at 200 rpm in an orbital shaker. Growth was monitored until OD600=0.5-0.7. At this point one flask was induced with IPTG (isopropyl-.β.-D-1-thiogalactopyranoside) to a final concentration 0.05 mM whilst the second flask was left un-induced to monitor basal expression. The incubation was continued, under the conditions described above, during which samples were taken for measurement of growth, accumulation of hTNFα within the bacterial cells. The accumulation level of hTNFα was determined using densitometry scanning of Colloidal Blue stained SDS-PAGE gels of whole cell lysates of the sampled bacteria. The results are summarised below in Table 3.










TABLE 3







Time (hours)
Accumulation Level of hTNFα (% TCP*)



















3
2



4
18



6
25



8
33



24 
42



24 (basal, no IPTG)
13







*TCP = Total Cell Protein






Taken together the data presented in Comparisons 1 and 2, and Example 3, show that effective control of the powerful T7A3 promoter was surprisingly achieved using a single perfect palindrome operator sequence. This was totally un-expected given that the use of the single native operator (Comparison 2) did not provide sufficient basal control to allow a stable recombinant production strain to be established. High product accumulation levels were achieved with the single perfect palindrome control system using relatively low concentration of inducer for induction. Although basal expression (in the absence of inducer) was observed it was evident only after significantly extended incubation (24 h).
EXAMPLE 4
Vials of CLD018 was removed from the −80° C. freezer and allowed to thaw. 10 μl of the thawed glycerol stock was inoculated into 5 ml Luria Broth (LB, 5 g/L yeast extract (Oxoid), 10 g/L tryptone (Oxoid), and 5 g/L sodium chloride) supplemented with tetracycline (10 μg/ml) and glucose (1 g/L). The seed culture was incubated at 37° C. in an orbital shaker for 16 h. 500 μl of the seed culture was then used to inoculate 250 ml Erlenmeyer flasks containing 50 ml of Luria Broth (composition as described above). The flasks were incubated at 37° C., at 200 rpm in an orbital shaker. Growth was monitored until OD600=0.5-0.7. At this point flasks were induced with IPTG (isopropyl-.β.-D-1-thiogalactopyranoside) to a final concentration 0.05 mM and 1 mM. A flask was also left un-induced and the incubation of the flasks continued, under the conditions described above, during which samples were taken for measurement of growth, accumulation of hTNFα within the bacterial cells. The accumulation level of hTNFα was determined using densitometry scanning of Colloidal Blue stained SDS-PAGE gels of whole cell lysates of the sampled bacteria. The results are summarised below in Table 4.










TABLE 4






Accumulation

Accumulation


0.05 mM IPTG
Level of hTNFα
1 mM IPTG
Level of hTNFα


Time (hours)
(% TCP)
Time (hours)
(% TCP)


















3
2
5
7


4
5
6
12


6
8
8
19


8
13
24
26


24 
19


24 (basal, no
Not detected


IPTG)









This data demonstrated that further control of the powerful T7A3 promoter could be realised using two perfect palindrome operator sequences spaced at 91 bp apart. Basal expression (in the absence of inducer) has been reduced significantly from that achieved using a single perfect palindrome operator to control repression. The control of basal expression achieved using the dual perfect palindrome sequences was un-expected when compared to the T7 system of U.S. Pat. No. 6,537,779 where control of basal expression requires two different control elements. In this example control of basal expression was achieved in a high background of E. coli RNA polymerase.
EXAMPLE 5
Vials of CLD026 was removed from the −80° C. freezer and allowed to thaw. 10 μl of the thawed glycerol stock was inoculated into 5 ml Luria Broth (LB, 5 g/L yeast extract (Oxoid), 10 g/L tryptone (Oxoid), and 5 g/L sodium chloride) supplemented with tetracycline (10 μg/ml) and glucose (1 g/L). This was incubated at 37° C. in an orbital shaker for 16 h. 500 μl of this culture was then used to inoculate 250 ml Erlenmeyer flasks containing 50 ml of Luria Broth (composition as described above). The flasks were incubated at 37° C., at 200 rpm in an orbital shaker. Growth was monitored until OD600=0.5-0.7. At this point flasks were induced with IPTG (isopropyl-.β.-D-1-thiogalactopyranoside) to a final concentration 0.05 mM and 0.005 mM. A flask was also left un-induced and the incubation continued, under the conditions described above, during which samples were taken for measurement of growth, accumulation of hTNFα within the bacterial cells. The accumulation level of hTNFα was determined using densitometry scanning of Colloidal Blue stained SDS-PAGE gels of whole cell lysates of the sampled bacteria. The results are summarised below in Table 5.










TABLE 5







0.005 mM



0.005 mM IPTG
Accumulation
IPTG
Accumulation


induction
Level of hTNFα
induction
Level of hTNFα


Time (hours)
(% TCP)
Time (hours)
(% TCP)







8
15
8
17


24 (basal, no IPTG)
Not detected









The results demonstrated that changing the spacing between the two perfect palindrome operator sequences by 1 bp (from 91 to 92 bp) did not adversely influence performance both in terms of basal expression and final accumulation level achieved. Unexpectedly, reducing the IPTG concentration 10 fold (from 0.05 mM to 0.005 mM) did not significantly reduce induced productivity.
EXAMPLE 6
Vials of CLD042 and CLD043 were removed from the −80° C. freezer and allowed to thaw. 10 μl of each of the thawed glycerol stock was inoculated separately into each of 2×5 ml Luria Broth (LB, 5 g/L yeast extract (Oxoid), 10 g/L tryptone (Oxoid), and 5 g/L sodium chloride) supplemented with tetracycline (10 μg/ml) and glucose (1 g/L). These were incubated at 37° C. in an orbital shaker for 16 h. 500 μl of these cultures were then used to separately inoculate 250 ml Erlenmeyer flasks containing 50 ml of Luria Broth (composition as described above). The flasks were incubated at 37° C., at 200 rpm in an orbital shaker. Growth was monitored until OD600=0.5-0.7. At this point flasks were induced with IPTG (isopropyl-.β.-D-1-thiogalactopyranoside) to a final concentration 0.5 mM. Flasks containing a culture of each strain were also left un-induced and the incubation continued, under the conditions described above, during which samples were taken for measurement of growth, accumulation of hTNFα within the bacterial cells. The accumulation level of hTNFα was determined using densitometry scanning of Colloidal Blue stained SDS-PAGE gels of whole cell lysates of the sampled bacteria. The basal accumulation level of hTNFα in the un-induced cultures of CLD042 and CLD043 after 20 hours incubation was compared by Western blot analysis (using anti-hTNFα antibody) following SDS-PAGE of the sampled bacteria. The blots were scanned and the data normalised to enable comparison. The results are summarised below in Table 6.








TABLE 6







CLD043: tac promoter,
CLD042: tac promoter, single


single native lac
perfect palindrome operator -


operator - 0.5 mM IPTG induction
0.5 mM IPTG induction











Accumulation

Accumulation



Level of hTNFα

Level of hTNFα


Time (hours)
(% TCP)
Time (hours)
(% TCP)













 3
6
 3
2


12
23
12
18


20
25
20
21








Western Blot: scan intensity*
Western Blot: scan intensity*










20
1
20
0.25


(Basal, no IPTG)

(Basal, no




IPTG)





*= scan of hTNFα band on Western blot. Intensity scan data for CLD042 normalised against the intensity scan data for CLD043.






The results demonstrated that the single perfect palindrome operator sequence can be used to reduce basal expression (in the absence of inducer) four fold without adversely influencing the induced productivity of the tac promoter system.
EXAMPLE 7
A vial of CLD019 was removed from the −80° C. freezer and allowed to thaw. 10 μl of the thawed glycerol stock was inoculated into 5 ml Luria Broth (LB, 5 g/L yeast extract (Oxoid), 10 g/L tryptone (Oxoid), and 5 g/L sodium chloride) supplemented with tetracycline (10 μg/ml) and glucose (1 g/L). This was incubated at 37° C. in an orbital shaker for 16 h. 500 μl of this culture was then used to inoculate 250 ml Erlenmeyer flasks containing 50 ml of Luria Broth (composition as described above). The flasks were incubated at 37° C., at 200 rpm in an orbital shaker. Growth was monitored until OD600=0.5-0.7. At this point the flasks were induced with IPTG (isopropyl-.β.-D-1-thiogalactopyranoside) to a final concentration 0.5 mM, 0.1 mM, 0.05 mM and 0.005 mM. A flask was also left un-induced and the incubation continued, under the conditions described above, during which samples were taken for measurement of growth, and accumulation of hTNFα within the bacterial cells. The accumulation level of hTNFα was determined using densitometry scanning of Colloidal Blue stained SDS-PAGE gels of whole cell lysates of the sampled bacteria. The results are presented in FIG. 2.
The data presented in FIG. 2 demonstrated that the combination of the tac promoter with dual perfect palindrome operator sequences lead to a system in which the expression rate can be modulated directly by the concentration of IPTG used for induction. Such systems may be exploited to modulate expression of heterologous proteins, for example, to maximise accumulation of proteins in a soluble form or to circumvent the problem of the deleterious effect that heterologous protein secretion can have on the growth and productivity of recombinant cells.
EXAMPLE 8
A vial of CLD030 was removed from the −80° C. freezer and allowed to thaw. 10 μl of the thawed glycerol stock was inoculated into 5 ml Luria Broth (LB, 5 g/L yeast extract (Oxoid), 10 g/L tryptone (Oxoid), and 5 g/L sodium chloride) supplemented with tetracycline (10 μg/ml) and glucose (1 g/L). This was incubated at 37° C. in an orbital shaker for 16 h. 500 μl of this culture was then used to inoculate 250 ml Erlenmeyer flasks containing 50 ml of Luria Broth (composition as described above). The flasks were incubated at 37° C., at 200 rpm in an orbital shaker. Growth was monitored until OD600=0.5-0.7. At this point a flask was induced with IPTG (isopropyl-.β.-D-1-thiogalactopyranoside) to a final concentration 0.05 mM whilst the other flask was left un-induced and the incubation continued, under the conditions described above, during which samples were taken for measurement of growth, accumulation of hTNFα within the bacterial cells. The accumulation level of hTNFα was determined using densitometry scanning of Colloidal Blue stained SDS-PAGE gels of whole cell lysates of the sampled bacteria. The results are summarised below in Table 7.










TABLE 7







Time (hours)
Accumulation Level of hTNFα (% TCP)









4
2



6
5



8
9



24 
12 



24 (basal, no IPTG)
Not detected










The data presented in Table 7 clearly show that control of the very powerful λpL promoter can be surprisingly achieved using a single perfect palindrome operator sequence. High product accumulation levels can be achieved using the single perfect palindrome control system.
EXAMPLE 9
Vials of CLD021 and CLD038 were removed from the −80° C. freezer and allowed to thaw. 10 μl of each of the thawed glycerol stock was inoculated separately into 5 ml Luria Broth (LB, 5 g/L yeast extract (Oxoid), 10 g/L tryptone (Oxoid), and 5 g/L sodium chloride) supplemented with tetracycline (10 μg/ml) and glucose (1 g/L). These were incubated at 37° C. in an orbital shaker for 16 h. 500 μl of this culture was then used to inoculate 250 ml Erlenmeyer flasks containing 50 ml of Luria Broth (composition as described above). The flasks were incubated at 37° C., at 200 rpm in an orbital shaker. Growth was monitored until OD600=0.5-0.7. At this point a flask was induced with IPTG (isopropyl-.β.-D-1-thiogalactopyranoside) to a final concentration 1 mM whilst a second flask was left un-induced and the incubation continued, under the conditions described above, during which samples were taken for measurement of growth, accumulation of hTNFα within the bacterial cells. The accumulation of hTNFα was determined using Colloidal Blue stained SDS-PAGE gels and Western blot analysis (using anti-hTNFα antibody) following SDS-PAGE of whole cell lysates of the sampled bacteria. The data are summarised in Table 8. The Western blot analysis for strain CLD038 is presented in FIG. 3.









TABLE 8






hTNFα




Accumulation -



CLD021
hTNFα Accumulation -CLD038


Analysis
(λpL:DPPS91)
(λpL:DPPS92)







Colloidal Blue
Not detected
Not detected


SDS-PAGE (post


IPTG induction)


Western blot
Positive
Positive (see FIG. 2)


(post IPTG


induction)


Colloidal Blue
Not detected
Not detected


SDS-PAGE


(Basal no IPTG


induction, 24 h)


Western blot
Not detected
Not detected


(Basal no IPTG


induction, 24 h)









These results demonstrated that the combination of dual perfect palindrome operator sequences with the λpL promoter with either the 91 bp or 92 bp spacing resulted in very tight repression. Western blots indicate that no basal expression of the target protein was detected. On induction low-level expression level was achieved. These results were totally unexpected given that the λpL promoter is an extremely powerful promoter. Such a system may, for example, be used to direct the expression of proteins of high toxicity to the host cell. It can be used when controlled expression is advantageous, for example, for the expression and insertion of membrane proteins.
EXAMPLE 10
Vials of CLD028 and CLD035 were removed from the −80° C. freezer and allowed to thaw. 10 μl of each of the thawed glycerol stock was inoculated separately into each of 2×5 ml Luria Broth (LB, 5 g/L yeast extract (Oxoid), 10 g/L tryptone (Oxoid), and 5 g/L sodium chloride) supplemented with tetracycline (10 μg/ml) and glucose (1 g/L). These were incubated at 37° C. in an orbital shaker for 16 h. 500 μl of these cultures were then used to separately inoculate 250 ml Erlenmeyer flasks containing 50 ml of Luria Broth (composition as described above). The flasks were incubated at 37° C., at 200 rpm in an orbital shaker. Growth was monitored until OD600=0.5-0.7. At this point flasks were induced with IPTG (isopropyl-.β.-D-1-thiogalactopyranoside) to a final concentration 1 mM and the incubation continued, under the conditions described above, during which samples were taken for measurement of growth, accumulation of hTNFα within the bacterial cells. The accumulation level of hTNFα was determined using densitometry scanning of Colloidal Blue stained SDS-PAGE gels of whole cell lysates of the sampled bacteria. The results are summarised below in Table 9.








TABLE 9







CLD035: T7A3 promoter, dual
CLD028: T7A3 promoter, dual


perfect palindrome operators
perfect palindrome operators


with 91 bp spacing
with 92 bp spacing










Time (hours)
Accumulation
Time (hours)
Accumulation


post IPTG
Level of hTNFα
post IPTG
Level of hTNFα


induction
(% TCP)
induction
(% TCP)













2
7
2
10


4
14
4
15


20
27
20
23









These data taken together with the data presented in Examples 4 and 5 previously indicated that both E. coli K-12 and B strains can be used.
EXAMPLE 11
Fermentation inocula were raised by adding 200 μl of glycerol stock of each of the strains described below to a 2.0 L baffled shake flask containing 200 mL of Luria Broth (LB, 5 g/L yeast extract (Oxoid), 10 g/L tryptone (Oxoid), and 5 g/L sodium chloride) supplemented with 15 μg/ml of tetracycline. Inocula were grown for 12 h at 37° C. in a shaker-incubator with an agitation of 250 rpm. 200 ml shake flask inoculum was used to inoculate a 15 L working volume fermenter containing 10 L of batch growth medium. Fermentations were carried out under the operating conditions described below. Temperature was controlled at 37° C. and pH at 6.8, controlled by automatic addition of 35% (w/v) ammonium hydroxide. The dissolved oxygen tension (dOT) set point was 30% of air saturation and was controlled by automatic adjustment of the fermenter stirrer speed, from a minimum of 250 rpm up to a maximum of 1500 rpm, and automatic supplementation of oxygen to the inlet gas stream. Airflow to the fermenter vessel was 10 L/min throughout. Pressure in the fermenter was maintained between 50 and 200 mbar.
Fermentations were performed in batch mode until depletion of the carbon source (i.e. glycerol) which occurred ca. 10 h post inoculation and was characterized by a sharp rise in dOT. Fed-batch fermentation was initiated at the point of carbon source exhaustion by the addition of a glycerol/magnesium chloride feed at a feed rate of 11 g of glycerol per L of medium per h. Induction was carried out by addition of IPTG to a final concentration of 0.5 mM once the biomass level in the fermentation reached OD600=50-60. The fed-batch phase was continued for 12 h post induction. Samples were taken to determine biomass level (OD600) and hTNFα accumulation (% TCP)/hTNFα titre (g/L) at harvest (Colloidal Blue stained SDS-PAGE gels).
The composition of the batch growth medium is provided in Table 10.










TABLE 10








Final concentration



Component
[g/L], mg/L] and [ml/L] of purified water




















(NH4)2SO4
14.0




Glycerol
35.0



Yeast extract
20.0



(Becton Dickinson)



KH2PO4
2.0



K2HPO4
16.5



Citric acid
7.5



MgSO4•7H2O
2.47



H3PO4
1.5
ml/L



CaCl2•2H2O
0.294



Antifoam AF204
0.2
ml/L



Tetracycline
15
mg/L



FeSO4•7H2O
114
mg/L



ZnSO4•7H20
29
mg/L



MnSO4•H20
17
mg/L



Na2MoO4•2H2O
9
mg/L



CuSO4•5H2O
4
mg/L



H3•BO3
12
mg/L










The composition of the glycerol/magnesium chloride feed is provided in Table 11.










TABLE 11








Amount required



Component of Feed
[g/L] of purified water



















Glycerol
714



MgSO4•7H2O
7.4










The results are summarised in Table 12. The hTNFα productivity profile for Strain CLD030 is presented in FIG. 4.











TABLE 12









hTNFα





hTNFα
titre




OD600
accumulation
(mg/L)



Expression vector
at
(% TCP) at
at


Strain
description
harvest
harvest
harvest



















CLD018
T7A3 promoter, dual
147
29
8400



perfect palindrome with



91 bp spacing


CLD026
T7A3 promoter, dual
204
34
11400



perfect palindrome with



92 bp spacing


CLD032
T7A3 promoter, single
194
41
12500



perfect palindrome



sequence


CLD019
tac promoter, dual perfect
196
22
8300



palindrome sequence with



91 bp spacing


CLD030
λpL promoter with single
167
7
2600



perfect palindrome



sequence









The data clearly demonstrate the utility of the systems for the manufacture of heterologous proteins. High product titres were achieved using a simple generic un-optimised fermentation and induction processes. The control characteristics of plasmid pAVE027, as demonstrated by productivity profile exemplified in FIG. 4, can be exploited to maximize the production of heterologous proteins, particularly proteins that require control of expression to maximize secretion.
EXAMPLE 12
A vial of CLD050 was removed from the −80° C. freezer and allowed to thaw. 10 μl of the thawed glycerol stock was inoculated into 5 ml Luria Broth (LB, 5 g/L yeast extract (Oxoid), 10 g/L tryptone (Oxoid), and 5 g/L sodium chloride) supplemented with tetracycline (10 μg/ml) and glucose (1 g/L). This was incubated at 37° C. in an orbital shaker for 16 h. 500 μl of this culture was then used to inoculate 250 ml Erlenmeyer flasks containing 50 ml of Luria Broth (composition as described above). The flasks were incubated at 37° C., at 200 rpm in an orbital shaker. Growth was monitored until OD600=0.5-0.7. At this point a flask was induced with IPTG (isopropyl-.β.-D-1-thiogalactopyranoside) to a final concentration 0.05 mM whilst another flask was left uninduced and the incubation continued, under the conditions described above, during which samples were taken for measurement of growth, accumulation of hTNFα within the bacterial cells. The accumulation level of hTNFα was determined using densitometry scanning of Colloidal Blue stained SDS-PAGE gels of whole cell lysates of the sampled bacteria. The results are summarised below in Table 13.








TABLE 13





Time post induction (hours)
Accumulation Level of hTNFα (% TCP)







4
16


24 (basal, no IPTG)
Not detected









Surprisingly the dual perfect palindrome operator sequence worked when the spacing was increased. The spacing of the dual perfect palindrome can be altered, for example, to achieve effective control of other promoters.
EXAMPLE 13
A vial of CLD048 was removed from the −80° C. freezer and allowed to thaw. 10 μl of the thawed glycerol stock was inoculated into 5 ml Luria Broth (LB, 5 g/L yeast extract (Oxoid), 10 g/L tryptone (Oxoid), and 5 g/L sodium chloride) supplemented with tetracycline (10 μg/ml) and glucose (1 g/L). This was incubated at 37° C. in an orbital shaker for 16 h. 500 μl of this culture was then used to inoculate a 250 ml Erlenmeyer flask containing 50 ml of Luria Broth (composition as described above). The flask was incubated at 37° C., at 200 rpm in an orbital shaker. Growth was monitored until OD600=0.5-0.7. At this point the flask was induced with IPTG (isopropyl-.β.-D-1-thiogalactopyranoside) to a final concentration of 0.1 mM and the incubation continued, under the conditions described above for a further 2 h. The cells and residual cell free growth medium were then harvested. The harvested cells were further subjected to osmotic shock cell fractionation to isolate the cellular fraction containing proteins that had partitioned in the soluble E. coli periplasmic fraction. The accumulation of biologically active D1.3 Fab in the soluble periplasmic extract and residual growth medium was estimated by determining the binding of D1.3 Fab to lysoszyme (antigen) in an ELISA assay by reference to a standard curve prepared with purified active D1.3 Fab. The accumulation of biologically active D1.3 Fab in the periplasm of E. coli and in the residual growth medium (due to leakage of material from the periplasm to the growth medium) is presented in Table 14. The accumulation of D1.3 Fab in the periplasm and residual growth medium was normalised as “μg active material per liter of culture per unit of biomass (OD600).










TABLE 14








Biologically active




D1.3 Fab (μg/L



Fraction
culture/OD)



















Residual growth medium
460



Periplasm
4020



Total (residual growth
4480



medium + periplasm)










The utility of the control provided by this system to enable high level secretion of heterologous proteins particularly those requiring complex disulphide bond formation is clearly exemplified by the secretion and accumulation of high levels of biologically active D1.3 Fab in the periplasm of E. coli. Additionally, it will be evident to those skilled in the art how fed-batch fermentation (for example, as described previously in Example 11 or below in Example 14) can be used to manufacture such proteins at high yield.

EXAMPLE 14
The fermentation process described in Example 11 was repeated using CLD048. Induction was carried out by addition of IPTG to a final concentration of 0.15 mM once the biomass level in the fermentation reached OD600=ca. 50. The fed-batch phase was continued for 35-45 h post induction. The cells and residual cell free growth medium were then harvested. The harvested cells were further subjected to osmotic shock cell fractionation to isolate the cellular fraction containing proteins that had partitioned in the soluble E. coli periplasmic fraction. The accumulation of biologically active D1.3 Fab in the soluble periplasmic extract and residual growth medium was estimated by determining the binding of D1.3 Fab to lysoszyme (antigen) in an ELISA assay by reference to a standard curve prepared with purified active D1.3 Fab. The accumulation of D1.3 Fab in the periplasm and residual growth medium was normalised as “mg active material per liter of culture”.
The accumulation of biologically active D1.3 Fab in the periplasm of E. coli and in the residual growth medium (due to leakage of material from the periplasm to the growth medium) is presented in Table 15.










TABLE 15








Biologically active



Fraction
D1.3 Fab (mg/L culture)



















Residual growth medium
525



Periplasm
57



Total (residuai growth
582



medium + periplasm)










High level secretion of biologically active D1.3 Fab is demonstrated using the expression system.

EXAMPLE 15
A synthetic bispecific single chain tetravalent diabody (bsctDb) was designed, in which the variable light and variable heavy regions from D1.3 (anti-lysozyme) and A5B7 (anti-CEA (carcinoembryonic antigen)), were linked on a single polypeptide chain. The DNA sequence for this molecule is shown in FIG. 5 (SEQ ID NO 22). This was cloned as an Nde I/Not I fragment into pAVE046 which had been digested with Nde I and Not I. Recombinant plasmids were screened by restriction digest and confirmed by sequencing. The resultant plasmid was named pAVE078. pAVE078 was transformed into E. coli W3110 to make CLD073, which was purified and maintained in glycerol stocks at −80° C.
A vial of CLD0073 was removed from the −80° C. freezer and allowed to thaw. 10 μl of the thawed glycerol stock was inoculated into 5 ml Luria Broth (LB, 5 g/L yeast extract (Oxoid), 10 g/L tryptone (Oxoid), and 5 g/L sodium chloride) supplemented with tetracycline (10 μg/ml) and glucose (1 g/L). This was incubated at 37° C. in an orbital shaker for 16 h. 500 μl of this culture was then used to inoculate two 250 ml Erlenmeyer flasks containing 50 ml of Luria Broth (composition as described above). The flasks were incubated at 37° C., at 200 rpm in an orbital shaker. Growth was monitored until OD600=0.5-0.7. At this point the flasks were induced with IPTG to a final concentration of either 0.5 mM or 0.1 mM and the incubation continued, under the conditions described above for a further 20 hours. The cells and residual cell free growth medium were then harvested. The harvested cells were further subjected to osmotic shock cell fractionation to isolate the cellular fraction containing proteins that had partitioned in the soluble E. coli periplasmic fraction. The expression, secretion, folding and accumulation of biologically active D1.3-A5B7 bsctDb in the periplasmic extract and residual growth medium was estimated by determining the inhibition of binding of an anti-CEA monoclonal antibody to CEA (antigen) in a competitive ELISA assay and by the binding of an anti-lysozyme Fab antibody fragment to lysozyme (antigen) in a competitive ELISA assay.
The data obtained indicated that the majority of D1.3-A5B7 bsctDb partitioned in the residual growth medium (leakage from the periplasm) at the end of the induction. This data (binding of bsctDb in competitive ELISA) is shown in Table 16. The data obtained demonstrates that the residual growth medium sample from the culture induced with 0.5 mM IPTG completely inhibits the binding of both the anti-CEA and anti-lysozyme antibodies in the competition ELISA assays. The residual growth medium sample from the culture induced with 0.1 mM IPTG shows a reduced level of inhibition indicating a lower accumulation level of biologically active D1.3-A5B7 bsctDb in this sample.









TABLE 16







% Inhibition in



% Inhibition in
D1.3 Competition


Sample
CEA Competition ELISA
ELISA







Control
None
None


(No D1.3-A5B7 bsctDb)


Supernatant from culture
100
100


induced with 0.5 mM IPTG


Supernatant from culture
Partial
Partial


induced with 0.1 mM IPTG









Using the new expression system it is possible to produce complex multi-chain heterologous proteins which have been difficult to produce using E. coli. This has been exemplified by demonstrating that bispecific single chain tetravalent diabodies in a biologically active form can be produced in E. coli using the new expression system. This further exemplifies the utility of the expression system.
EXAMPLE 16
The glutathione-S-transferase-3C proteinase fusion (GST-3C) gene was cloned as an Nde I/Xho I fragment into pAVE011 digested with Nde I and Xho I. The sequence of the insert is shown in FIG. 6 (SEQ ID NO 23). Recombinant plasmids were screened by restriction digest and confirmed by sequencing. The resultant plasmid was named pAVE052. pAVE052 was transformed into E. coli BL21 to make CLD054, which was purified and maintained in glycerol stocks at −80° C.
The human Interferon α2 (IFNα2) gene was cloned as an Nde I/Xho I fragment into pAVE011 digested with Nde I and Xho I. The DNA sequence of the insert is shown in FIG. 7 (SEQ ID NO 24). Recombinant plasmids were screened by restriction digest and confirmed by sequencing. The resultant plasmid was named pAVE058. pAVE058 was transformed into E. coli W3110 to make CLD059, which was purified and maintained in glycerol stocks at −80° C.
The human erythropoietin (EPO) gene, which had been codon optimised for expression in E. coli, was cloned as an Nde I/Xho I fragment into pAVE011 digested with Nde I and Xho I. The DNA sequence of the insert is shown in FIG. 8 (SEQ ID NO 25). Recombinant plasmids were screened by restriction digest and confirmed by sequencing. The resultant plasmid was named pAVE061. pAVE061 was transformed into E. coli W3110 to make CLD060, which was purified and maintained in glycerol stocks at −80° C.
Fed-batch fermentations using CLD054, CLD059 and CLD060 were carried out using the media and process conditions described in Example 11 Fermentations were maintained at 30° C. or 37° C. as described in Table 19. Fermentations were performed in batch mode until depletion of the carbon source (i.e. glycerol). Fed-batch fermentation was initiated at this point by the addition of a feed containing glycerol (714 g/L) and magnesium sulphate (30 g/L). Induction was carried out by addition of IPTG once the biomass level in the fermentation reached OD600=50-60. The IPTG concentrations used are described in Table 17. The fed-batch phase was continued for 12-15 h post induction. Samples were taken throughout the fermentations to determine biomass level (OD600) and protein product ((GST-3C, IFNα2 and EPO) titre (g/L), using Colloidal Blue stained SDS-PAGE gels of whole cell lysates of the sampled bacteria).













TABLE 17







Protein and

Induction

Prod-




Expression
Ferm
IPTG

uct



E. coli
Vector
Temp
Conc

Titre


Strain
Host
Description
° C.
(mM)
OD600
(g/L)





















CLD054
BL21
GST-3C
37
0.50
100
8




T7A3:DPPS91


CLD059
W3110
IFNα2
37
0.10
120
9




T7A3:DPPS91
37
0.25
150
14





37
0.50
160
14


CLD060
W3110
EPO
37
0.10
100
>13




T7A3:DPPS91
30
0.50
90
>13









The data presented in Table 17 further demonstrate the utility of the systems for the manufacture of a wide range of heterologous proteins. High product titres are achieved using a simple generic fermentation process coupled with manipulation of only the concentration of IPTG used for induction. This is particularly beneficial to reduce the process development timelines for therapeutically useful heterologous proteins.

EXAMPLE 17
The L-2-haloalkanoate dehalogenase (hadL) gene from Pseudomonas putida was cloned using Nde I and Spe I sites that had been engineered using PCR. The gene sequence is shown in FIG. 9 (SEQ ID NO 26). Plasmid pAVE011 was digested with Nde I and Spe I and the band was gel extracted. The hadL gene was digested with Nde I and Spe I and the hadL gene was gel extracted and ligated to pAVE011 to produce pAVE075. The Pseudomonas savastanoi origin of replication was copied using the PCR from Plasmid pCN60 (ATCC 77101; Nieto C, et al. (1990) Gene 87: 145-149).
The primers used were:







(SEQ ID NO 27)


F37A: Sequence: 5′AGATCTACGCTTATGGGTGCCTTTCC,


and


 


(SEQ ID NO 28)


B29a: Sequence: 5′AGATCTAATACGCAAACCGCCTCTCC.






The PCR product was cloned initially into TOPO TA pCR2.1 (Invitrogen) and then into pAVE075 by Bgl II digestion. The resultant plasmid, pAVE086 was transformed into Pseudomonas putida NCIMB 12018, via electroporation to make CLD075, which was purified and maintained in glycerol stocks at −80° C. A vial of CLD075 was removed from a −80° C. freezer and allowed to thaw. 10 μl of the thawed glycerol stock was inoculated into 5 ml Luria Broth (LB, 5 g/L yeast extract (Oxoid), 10 g/L tryptone (Oxoid), and 5 g/L sodium chloride) supplemented with tetracycline (10 μg/ml). This was incubated at 30° C. in an orbital shaker for 16 h. 500 μl of this culture was then used to separately inoculate two 250 ml Erlenmeyer flasks containing 50 ml of Luria Broth (composition as described above). The flasks were incubated at 30° C., at 200 rpm in an orbital shaker. Growth was monitored until OD600=0.5-0.7. At this point one flask was induced with IPTG to a final concentration 0.5 mM whilst the second flask was left un-induced to monitor basal expression. The incubation was continued, under the conditions described above, during which samples were taken for measurement of growth and accumulation of HadL protein within the bacterial cells. The accumulation level of HadL was determined using densitometry scanning of Colloidal Blue stained SDS-PAGE gels of whole cell lysates of the sampled bacteria.
The expression and accumulation of HadL protein is presented in FIG. 10. The data indicate that the T7A3:DPPS91 expression system functioned in another prokaryotic host system. Surprisingly, the expression system performed with the same efficiency in Pseudomonas putida as that observed when using E. coli as the host system. Basal expression was not detected even following 23 h incubation in the absence of inducer. High level protein expression and accumulation was achieved in Pseudomonas putida following induction using IPTG.
EXAMPLE 18
Fed-batch fermentation using Pseudomonas putida CLD075 was carried out using the generic E. coli media and process conditions described in Example 11. Fermentations were maintained at 30° C. and pH 7.0 (controlled with 25% ammonium hydroxide and 10% phosphoric acid). Fermentations were performed in batch mode until depletion of the carbon source (i.e. glycerol). Fed-batch fermentation was initiated at this point by the addition of a feed containing glycerol (714 g/L) and magnesium sulphate (30 g/L). Induction was carried out by addition of 1 mM IPTG (final concentration) once the biomass level in the fermentation reached OD600=50. The fed-batch phase was continued for 12-15 h post induction. Samples were taken throughout the fermentation to determine biomass level (OD600) and HadL protein accumulation ((% TCP) Colloidal Blue stained SDS-PAGE gels of whole cell lysates of the sampled bacteria). The growth of CLD075 and expression/accumulation of HadL protein following induction are presented in FIG. 11.
High levels of protein expression and accumulation (>40% TCP) were achieved using the expression system in Pseudomonas putida even by just using a generic growth medium designed for use with E. coli. 
EXAMPLE 19
A synthetic Gal repressor gene (E. coli was cloned into vector pZenO42 (as described in EP 0 502 637) as a PstI fragment into the PstI site. Clones were identified with the Gal repressor gene in both clockwise and anticlockwise orientations. A clone with anticlockwise orientation was selected to generate pAVE071.
Construction of the Gal promoter and operator sequences was initiated in plasmid pZT7#2.0, prepared as described in U.S. Pat. No. 6,537,779. pZT7#2.0 has a pAT153 vector backbone, cer stability sequence, tet A/R, a single native lac operator sequence upstream of the gene of interest and an upstream T4 transcription terminator. The native Gal operator sequence was modified to produce a perfect palindromic operator sequence. This was cloned into the plasmid described above using synthetic linkers by means of EcoRI and XbaI restriction enzyme sites. The linker GalB was prepared by annealing the oligonucleotides GalB1 and GalB2:







(SEQ ID NO 29)


GalB1 


5′AATTCATACCATAAGCCTAATTCTACGAATTATCAGAGTTCTGGTTAC


 


CGGTGTAAGCGCTTACACTGT


 


(SEQ ID NO 30)


GalB2 


5′CTAGACAGTGTAAGCGCTTACACCGGTAACCAGAACTCTGATAATTCG


 


TAGAATTAGGCTTATGGTATG






The linker was then ligated to plasmid pZT7#2.0 and transformed into cloning host strain XL-1 Blue MR (Stratagene) as an EcoR I/Xba I fragment. Initial screening of transformants was by restriction digestion using AgeI. The sequence was confirmed by sequencing. The hTNFα gene was cloned into this plasmid as a NdeI/XhoI fragment.
The hTNFα gene and partial Gal perfect palindromic operator sequence were cloned by digesting with XmaI and MscI and ligating into pAVE071 digested with XmnI and XmaI. Clones were screened for the presence of the hTNFα gene by restriction digestion.
Upstream perfect palindromic Gal operator and Gal promotor were each cloned into this plasmid using synthetic linkers by means of StuI and EcoRI sites. Linker GalA was prepared by annealing the oligonucleotides GalA1 and GalA2:







GalA1 (SEQ ID NO 31):


5′CAATTGTGTAAGCGCTTACACAACTTTATTCCATGTCACACTTTTCGC


 


ATCTTTGTTATGCTATGGTG


 


(SEQ ID NO 32)


GalA2 


5′AATTCACCATCGCATAACAAGGATGCGAAAAGTGTGACATGGAATAAA


 


GTTGTGTAAGCGCTTACACAATTG






The presence of the linker was detected with digestion with MfeI and confirmed by sequencing. This plasmid was transformed into E. coli strain W3110 to generate CLD085 which was purified and maintained in glycerol stocks at −80° C.
A vial of CLD085 was removed from the −80° C. freezer and allowed to thaw. 10 μl of the thawed glycerol stock was inoculated into 5 ml Luria Broth (LB, 5 g/L yeast extract (Oxoid), 10 g/L tryptone (Oxoid), and 5 g/L sodium chloride) supplemented with tetracycline (10 μg/ml). This was incubated at 37° C. in an orbital shaker for 16 h. 500 μl of this culture was then used to inoculate a 250 ml Erlenmeyer flask containing 50 ml of Luria Broth (composition as described above). The flask was incubated at 37° C., at 200 rpm in an orbital shaker. Growth was monitored until OD600=0.5-0.7. At this point the flask was induced with galactose to a final concentration 10.0 mM. The incubation was continued, under the conditions described above, during which samples were taken for measurement of growth, accumulation of hTNFα within the bacterial cells. The accumulation level of hTNFα was determined using Western blot analysis (using anti-hTNFα antibody) following SDS-PAGE of the sampled bacteria. The data are presented in FIG. 17. This demonstrates that using perfectly palindromic gal operator sequences in combination with a gal repressor gene leads to very tight repression of the gal promoter in the absence of inducer whilst surprisingly still maintaining the capacity for induction when the inducer galactose is added.
EXAMPLE 20
A non-integrating yeast vector was constructed as follows:
1) Clone Sequence 1 (E. coli Lac I downstream of a Saccharomyces cerevisiae CYC1 promoter) as a Xho I fragment into Xho I digested pCR2.1 (Invitrogen). Clone Sequence 1 is shown in FIG. 15 (SEQ ID NO 35).
2) Clone Sequence 2 (which consists of the Saccharomyces cerevisiae MF-α1 gene promoter with perfect palindromic lac operator sequences either side of the MF-α1 promoter region, with the gene sequence for the protein elafin with a C-terminal c-myc tag (elafin-cmyc) positioned downstream) as a Hind III fragment (made by PCR) into Hind III digested plasmid constructed in Step 1 to produce plasmid 2. Clone Sequence 2 is shown in FIG. 16 (SEQ ID NO 36).
3) Clone the Spe I fragment from YEp13 (ATCC37115), containing the LEU2 (selection marker gene) and the yeast 2μ origin of replication, into SpeI digested plasmid 2 to generate pAVE091.
pAVE091 plasmid DNA was transformed into Saccharomyces cerevisiae XS95-6C (ATCC 204688) by electroporation and positive colonies selected on yeast drop-out medium without leucine (Kaiser C, Michaelis S and Mitchel A (Methods in Yeast Genetics, Cold Spring Harbor Laboratory Manual, 1994)). Shake flask growth studies to determine elafin-cmyc protein expression were carried out using the same medium. The flasks were incubated at 30° C., at 200 rpm in an orbital shaker. The clones were grown to an OD of  ̃3 and induced with 0.5 mM IPTG (final concentration). The incubation was continued for a further 16 h, under the conditions described above, during which samples were taken for measurement of growth and secretion of elafin-cmyc protein into the growth medium. The secretion of elafin-cmyc into the residual growth medium was determined using an elastase inhibition enzyme assay, as described in Wiedow O, et al, J Biol Chem. (1990) 265(25):14791-5. After 4 hours of IPTG induction there was 30 mg/L of active elafin protein in the growth medium. This demonstrates that the expression systems of the present invention are effective in yeasts.
EXAMPLE 21
A DNA fragment was synthesised which contained the constitutive human Cytomegalovirus (hCMV) promoter flanked by dual perfect palindromic lac operator sequences. This was cloned into an expression vector, which expressed IgG Fc protein. The resulting plasmid was named pAVE081, and is derived from pCMV-Script (Stratagene) and contains the hCMV promoter flanked by dual perfect palindromic lac operator sequences on a Nde I/Nhe I fragment, with the IgG Fc DNA sequence in the multiple cloning site of the vector. The DNA sequence of the hCMV promoter and dual perfect palindromic lac operators is shown in FIG. 12 (SEQ ID NO 33). The DNA sequence of the IgG Fc protein is shown in FIG. 13 (SEQ ID NO 34). Transient co-transfections of pAVE081 expressing IgG Fc protein and pCMVlacI (Stratagene) which expresses lac repressor were carried out, as is well described in the art, to determine whether IgG Fc protein could be expressed under the control an IPTG inducible hCMV promoter-dual perfect palindromic lac operator expression system.
2 ml of Chinese Hamster Ovary (CHO cell line ECACC 85050302 adapted to suspension growth in serum free medium) suspension culture at 1.5×105 viable cells per ml was added to each well of 6-well tissue culture plates. The 6-well tissue culture plates were then incubated overnight (16 h) in a humidified 37° C. incubator with 5% CO2 before transfection mixes were prepared containing 2 μg of pAVE081 DNA with an equal quantity of pCMVlacI (Stratagene) DNA, 6 μl of transfection reagent and 94 μl of growth medium per well. 100 μl of transfection mix was added to each well containing the CHO cells. The 6-well tissue culture plates were then incubated in humidified 37° C. incubator with 5% CO2. To determine the level of expression/secretion of IgG Fc protein into the growth medium a set of wells (day 2) were induced with 5 mM IPTG (final concentration) and set of wells left un-induced. On day three the set of wells induced with IPTG and those left un-induced were sampled (post IPTG induction and un-induced). The expression and secretion into the growth medium by the CHO cells of IgG Fc protein was determined by ELISA as is well established in the art. The data obtained are shown in FIG. 14.
The data clearly demonstrates the broad utility of the expression system. The expression system can be used to control powerful constitutive promoters typically used with mammalian cell systems, such as the hCMV promoter, to express proteins in mammalian cells in a controllable, inducible manner.

## Claims

1. A perfect palindrome operator sequence-based protein expression system comprising an E. coli host cell comprising:
(a) a T7A3 or tac RNA-polymerase dependent promoter; and
(b) two or more perfect palindrome operator sequences, at least one of the operator sequences being located downstream of the promoter, and at least one of the operator sequences being located upstream of the promoter;

wherein the operator sequence upstream of the promoter and the operator sequence downstream of the promoter are spaced 91 or 92 base pairs apart, and wherein an operator sequence overlaps the transcriptional start point.

2. A plasmid comprising:
(a) a T7A3 or tac RNA-polymerase dependent promoter; and
(b) two or more perfect palindrome operator sequences, at least one of the operator sequences being located downstream of the promoter, and at least one of the operator sequences being located upstream of the promotor;

wherein the operator sequence upstream of the promoter and the operator sequence downstream of the promoter are spaced 91 or 92 base pairs apart, and wherein an operator sequence overlaps the transcriptional start point.

3. A plasmid according to claim 2, further comprising an expression cassette for a protein.

4. A plasmid according to claim 2, wherein the plasmid is an autonomously replicating plasmid.

5. A plasmid according to claim 2, wherein the plasmid is an integrative plasmid.

6. A host cell transformed by a plasmid as claimed in claim 2.

7. A method for the production of a protein which comprises expressing an expression system comprising an E. coli host cell comprising:
(a) a T7A3 or tac RNA-polymerase dependent promoter;
(b) two or more perfect palindrome operator sequences; and
(c) an expression cassette for recombinant proteins, at least one of the operator sequences being located downstream of the promoter, and at least one of the operator sequences being located upstream of the promoter;

wherein the operator sequence upstream of the promoter and the operator sequence downstream of the promoter are spaced 91 or 92 base pairs apart, and wherein an operator sequence overlaps the transcriptional start point.

8. A method according to claim 7, wherein two perfect palindrome operator sequences are employed.

9. A method for producing a protein, which comprises:
(a) culturing an E. coli host cell transformed with the plasmid according to claim 3; and
(b) recovering the protein.

10. A method according to claim 9, wherein the operator sequences are perfect palindromic lac, gal, deo or gln sequences.

11. An expression system according to claim 1, wherein two perfect palindrome operator sequences are employed.

12. An expression system according to claim 1, wherein the operator sequences are perfect palindromic lac, gal, deo or gln sequences.

13. A plasmid according to claim 2, wherein two perfect palindrome operator sequences are employed.

14. A plasmid according to claim 2, wherein the operator sequences are perfect palindromic lac, gal, deo or gln sequences.

15. A host cell according to claim 6, wherein the operator sequences are perfect palindromic lac, gal, deo or gln sequences.

16. A perfect palindrome operator sequence-based recombinant protein expression system comprising an E. coli host cell comprising:
(a) a T7A3 promoter; and
(b) two perfect palindrome operator sequences, one of the operator sequences being located downstream of the promoter, and one of the operator sequences being located upstream of the promoter;

wherein the operator sequence upstream of the promoter and an operator sequence downstream of the promoter are spaced 91 or 92 base pairs apart, and wherein an operator sequence overlaps the transcriptional start point.

17. A plasmid comprising:
(a) a T7A3 promoter; and
(b) two perfect palindrome operator sequences, one of the operator sequences being located downstream of the promoter, and one of the operator sequences being located upstream of the promoter;

wherein the operator sequence upstream of the promoter and the operator sequence downstream of the promoter are spaced 91 or 92 base pairs apart, and wherein an operator sequence overlaps the transcriptional start point.

18. A method for the production of a recombinant protein which comprises expressing an expression system comprising an E. coli host cell comprising:
(a) a T7A3 promoter; and
(b) two perfect palindrome operator sequences, one of the operator sequences being located downstream of the promoter, and one of the operator sequences being located upstream of the promoter; and
(c) an expression cassette for a recombinant proteins;

wherein the operator sequence upstream of the promoter and the operator sequence downstream of the promoter are spaced 91 or 92 base pairs apart, and wherein an operator sequence overlaps the transcriptional start point.