# Patent

## Title
Production of proteins and polypeptides

## Abstract

A method of producing a desired non-spidroin protein or polypeptide is comprising the steps of expressing in a suitable host a fusion protein, obtaining a mixture containing the fusion protein, and optionally isolating the fusion protein. The fusion protein is comprising at least one solubility-enhancing moiety which is derived from the N-terminal (NT) fragment of a spider silk protein. It is further comprising at least one moiety which is a desired non-spidroin protein or polypeptide. Each solubility-enhancing moiety is linked directly or indirectly to the desired protein or polypeptide moiety.

## Background
TECHNICAL FIELD OF THE INVENTION
The present invention relates to the field of production of proteins and polypeptides, and more specifically to production of spider silk proteins (spidroins) and other, non-spidroin proteins and polypeptides. The present invention provides a method of producing a desired protein, which may be a spidroin protein/polypeptide or a non-spidroin protein/polypeptide. There is also provided novel fusion protein intermediates for production of the desired proteins and polypeptides as well as polynucleic acid molecules encoding these intermediates.
REFERENCE TO SEQUENCE LISTING SUBMITTED VIA EFS-WEB
This application is being filed electronically via EFS-Web and includes an electronically submitted sequence listing in .txt format. The .txt file contains a sequence listing entitled “2015-06-11 0104-0859PUS1 —ST25.txt” created on Jun. 11, 2015 and is 188,568 bytes in size. The sequence listing contained in this .txt file is part of the specification and is hereby incorporated by reference herein in its entirety.
BACKGROUND TO THE INVENTION
Production of proteins and polypeptides from DNA can be achieved in various hosts, but a common problem is the formation of insoluble protein/polypeptide aggregates. This may severely impede or even prevent production of a functional protein/polypeptide. One solution to this problem is to express the desired protein or polypeptide as a fusion protein with a protein or polypeptide that provides the required solubility. The fusion protein may be cleaved, and the desired protein isolated.
The problem is typically aggravated with low-solubility proteins and polypeptides, e.g. membrane-associated proteins and polypeptides. For instance, lung surfactant protein C (SP-C; Table 6) is a transmembrane protein that is produced by alveolar type II cells and is a constituent of surfactant, that is necessary to prevent alveolar collapse at end expiration. Neonatals often suffer from respiratory distress due to insufficient amounts of surfactant. Today, this condition is treated with surfactant preparations extracted from animal lungs. SP-C-33 is a variant of SP-C, where the residues in the transmembrane helix (normally mainly valines) are exchanged for leucines. SP-C-33 retains the function of native SP-C, including proper insertion in membranes, but is less prone to aggregate and therefore feasible to produce in large quantities for development of a synthetic surfactant preparation. Since SP-C-33 so far has not been possible to produce from DNA, it is today manufactured by chemical synthesis.
Other examples of proteins and polypeptides that pose difficulties when expressed from recombinant DNA are Aβ-peptide, IAPP, PrP, α-synuclein, calcitonin, prolactin, cystatin, ATF and actin; SP-B, α-defensins and β-defensins; class A-H apolipoproteins; LL-37, SP-C, SP-C33Leu, Brichos, GFP, neuroserpin; hormones, including EPO and GH, and growth factors, including IGF-I and IGF-II; avidin and streptavidin; and protease 3C.
SUMMARY OF THE INVENTION
It is an object of the present invention to provide new means and methods for production of proteins and polypeptides, and in particular non-spidroin proteins and polypeptides.
It is also an object of the present invention to provide new means and methods for production of proteins and polypeptides, and in particular non-spidroin proteins and polypeptides, with low solubility in water, e.g. proteins and polypeptides that are prone to aggregate when produced from recombinant DNA, membrane proteins and polypeptides, and amyloid-forming proteins and polypeptides.
It is a further object of the present invention to provide alternative means and methods for production of protein or polypeptide drugs and drug targets.
It is an object of the present invention to provide new means and methods for production of disulphide-containing proteins and polypeptides.
It is also an object of the present invention to provide new means and methods for production of apolipoproteins.
For these and other objects that will be evident from the following specification, the present invention provides according to a first aspect a fusion protein that is useful in a method of producing a desired protein or polypeptide. The fusion protein may be useful as such, or it may be cleaved to obtain the desired protein or polypeptide in isolated form. Fusion proteins according to the invention are comprising (i) at least one solubility-enhancing moiety which is derived from the N-terminal (NT) fragment of a spider silk protein; and (ii) at least one moiety which is a desired protein or polypeptide; wherein each solubility-enhancing moiety is linked directly or indirectly to the desired protein or polypeptide moiety.
In certain embodiments of the fusion protein, each solubility-enhancing moiety has at least 80% identity to SEQ ID NO 6 or at least 50% identity to SEQ ID NO 8. In specific embodiments of the fusion protein, each solubility-enhancing moiety contains from 100 to 160 amino acid residues.
In one embodiment, the fusion protein is subject to the proviso that when the fusion protein comprises a single solubility-enhancing moiety which is derived from the N-terminal (NT) fragment of a spider silk protein, then the desired protein or polypeptide is a non-spidroin protein or polypeptide.
In preferred embodiments, the desired protein or polypeptide is a non-spidroin protein or polypeptide. In some embodiments, the desired protein or polypeptide has less than 30% identity to any of SEQ ID NO: 6-10.
In certain embodiments, the fusion protein is comprising at least two solubility-enhancing moieties, each being derived from the N-terminal (NT) fragment of a spider silk protein. In specific embodiments, the fusion protein is comprising at least two consecutive solubility-enhancing moieties, each being derived from the N-terminal (NT) fragment of a spider silk protein.
In some embodiments of the fusion protein, at least one solubility-enhancing moiety is linked directly or indirectly to the amino-terminal or the carboxy-terminal end of at least one desired protein or polypeptide moiety. In specific embodiments, at least one solubility-enhancing moiety constitutes the amino-terminal and/or the carboxy-terminal end of the fusion protein.
In one embodiment, the fusion protein is further comprising (iii) at least one cleavage site arranged between at least one desired protein or polypeptide moiety and at least one solubility-enhancing moiety.
In certain embodiments of the fusion protein, the desired protein or polypeptide is derived from sponges, comb jellies, jellyfishes, corals, anemones, flatworms, rotifers, roundworms, ribbon worms, clams, snails, octopuses, segmented worms, crustaceans, insects, bryozoans, brachiopods, phoronids, sea stars, sea urchins, tunicates, lancelets, vertebrates, including human, plants, fungi, yeast, bacteria, archaebacteria or viruses or is an artificial protein or polypeptide. In specific embodiments, the desired protein or polypeptide is derived from molluscs, insects, vertebrates, including human, plants, fungi, yeast, bacteria, archaebacteria or viruses or is an artificial protein or polypeptide. In further specific embodiments, the desired protein or polypeptide is derived from vertebrates, including human, plants, fungi, yeast, bacteria, archaebacteria or viruses or is an artificial protein or polypeptide.
In some embodiments of the fusion protein, the desired protein or polypeptide is selected from the group consisting of amyloid-forming proteins and polypeptides, disulphide-containing proteins and polypeptides, apolipoproteins, membrane proteins and polypeptides, protein and polypeptide drugs and drug targets, aggregation-prone proteins and polypeptides, and proteases. In specific embodiments of the fusion protein, the desired protein or polypeptide is selected from the group consisting of Aβ-peptide, IAPP, PrP, α-synuclein, calcitonin, prolactin, cystatin, ATF and actin; SP-B, α-defensins and β-defensins; class A-H apolipoproteins; LL-37, SP-C, SP-C33, SP-C33Leu, Brichos, GFP, neuroserpin; hormones, including EPO and GH, and growth factors, including IGF-I and IGF-II; avidin and streptavidin; and protease 3C.
Preferred embodiments of the fusion protein are selected from the group consisting of SEQ ID NOS 26, 28, 30, 34, 37, 39, 42 and 47 and proteins having at least 80%, preferably at least 90%, more preferably at least 95% identity, to any of these proteins.
According to a specific aspect, the desired protein or polypeptide is a spidroin protein or polypeptide. A preferred desired spidroin protein is comprising: a repetitive fragment of from 70 to 300 amino acid residues derived from the repetitive fragment of a spider silk protein; and a C-terminal fragment of from 70 to 120 amino acid residues, which fragment is derived from the C-terminal fragment of a spider silk protein, and optionally an N-terminal fragment of from 100 to 160 amino acid residues derived from the N-terminal fragment of a spider silk protein.
A further preferred desired spidroin protein is selected from the group of proteins defined by the formulas REP-CT and NT-REP-CT, wherein NT is a protein fragment having from 100 to 160 amino acid residues, which fragment is a N-terminal fragment derived from a spider silk protein; REP is a protein fragment having from 70 to 300 amino acid residues, wherein said fragment is selected from the group of L(AG)nL, L(AG)nAL, L(GA)nL, L(GA)nGL, wherein n is an integer from 2 to 10; each individual A segment is an amino acid sequence of from 8 to 18 amino acid residues, wherein from 0 to 3 of the amino acid residues are not Ala, and the remaining amino acid residues are Ala; each individual G segment is an amino acid sequence of from 12 to 30 amino acid residues, wherein at least 40% of the amino acid residues are Gly; and each individual L segment is a linker amino acid sequence of from 0 to 20 amino acid residues; and CT is a protein fragment having from 70 to 120 amino acid residues, which fragment is a C-terminal fragment derived from a spider silk protein.
According to another aspect, the present invention provides isolated polynucleic acids encoding the fusion proteins according to the invention. Preferred embodiments of the isolated polynucleic acids are selected from the group consisting of nucleic acids encoding a fusion protein selected from the group consisting of SEQ ID NOS 26, 28, 30, 34, 37, 39, 42 and 47 and proteins having at least 80%, preferably at least 90%, more preferably at least 95% identity, to any of these proteins; and the group of nucleic acids consisting of SEQ ID NOS 27, 29, 31, 38, 40, 43 and 48.
According to one aspect, the present invention provides a novel use of at least one moiety which is derived from the N-terminal (NT) fragment of a spider silk protein as a solubility enhancing moiety in a fusion protein for production of a desired protein or polypeptide. In a preferred embodiment, the desired protein or polypeptide is a non-spidroin protein or polypeptide. In one embodiment, the fusion protein is subject to the proviso that when the fusion protein comprises a single solubility-enhancing moiety which is derived from the N-terminal (NT) fragment of a spider silk protein, then the desired protein or polypeptide is a non-spidroin protein or polypeptide. In a specific embodiment, the desired protein or polypeptide is a spidroin protein or polypeptide.
According to another aspect, the present invention provides a method of producing a fusion protein, comprising the following steps: a) expressing in a suitable host a fusion protein according to the invention; and b) obtaining a mixture containing the fusion protein, and optionally isolating the fusion protein.
According to a related aspect, the present invention provides a method of producing a desired protein or polypeptide, comprising the following steps: a) expressing in a suitable host a fusion protein according to the invention; and b) obtaining a mixture containing the fusion protein or polypeptide, and optionally isolating the fusion protein or polypeptide. In certain embodiments, this method is further comprising the following steps: c) cleaving the fusion protein to provide the desired protein or polypeptide; and d) isolating the desired protein or polypeptide; wherein said fusion protein is comprising: (iii) at least one cleavage site arranged between at least one desired protein or polypeptide moiety and at least one solubility-enhancing moiety.
In certain embodiments of these methods, step b) further involves purification of the fusion protein on an affinity medium with an immobilized NT moiety and/or on an anion exchange medium. In specific embodiments, the purification of the fusion protein on an affinity medium is carried out with association to an affinity medium with an immobilized NT moiety at a pH of 6.3 or lower, followed by dissociation from the affinity medium with a desired dissociation medium. In further specific embodiments, the dissociation medium has a pH of 6.4 or higher, a pH of 4.1 or lower and/or has a high ionic strength. In some embodiments, purification of the fusion protein on an anion exchange medium is carried out with association to the anion exchange medium at a pH of 6.4 or higher, followed by dissociation from the anion exchange medium with a dissociation medium having a high ionic strength. In some embodiments of these methods, the purification of the fusion protein in step b) occurs in a column, on magnetic beads with functionalized surfaces, or on filters with functionalized surfaces.
LIST OF APPENDED SEQUENCES











SEQ ID NO
















1
4Rep


2
4RepCT


3
NT4Rep


4
NT5Rep


5
NT4RepCTHis


6
NT


7
CT


8
consensus NT sequence


9
consensus CT sequence


10
repetitive sequence from



Euprosthenops australis MaSp1


11
consensus G segment sequence 1


12
consensus G segment sequence 2


13
consensus G segment sequence 3


14
NT4Rep (DNA)


15
NT4RepCT (DNA)


16
NT5Rep (DNA)


17
NT4RepCTHis 2


18
NT4RepCTHis 2 (DNA)


19
ZbasicNT4RepCT


20
NT4RepCT


21
HisTrxHisThrNT4RepCT


22
NT4RepCT 2


23
HisNTNT4RepCT


24
HisNTNT4RepCT (DNA)


25
NT8RepCT


26
HisNTMetSP-C33Leu


27
HisNTMetSP-C33Leu (DNA)


28
HisNTNTMetSP-C33Leu


29
HisNTNTMetSP-C33Leu (DNA)


30
HisNTNTMetLL37


31
HisNTNTMetLL37 (DNA)


32
NTHis


33
HisNTNT8RepCT


34
HisNTNTBrichos


35
HisTrxHisSP-C33Leu


36
HisTrxHisSP-C33Leu (DNA)


37
HisTrxNtSP-C33Leu


38
HisTrxNtSP-C33Leu (DNA)


39
2HisNtNtQGBrichos


40
2HisNtNtQGBrichos (DNA)


41
Brichos


42
2HisNtNtQGGFP


43
2HisNtNtQGGFP (DNA)


44
GFP (Green Fluorescent Protein)


45
ZbGFP


46
HisABPGFP


47
2HisNtNtQGNS


48
2HisNtNtQGNS (DNA)


49
NS (Neuroserpin)












BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 (SEQ ID NOS: 50-63)shows a sequence alignment of spidroin N-terminal domains.
FIG. 2 (SEQ ID NOS: 68-98)shows a sequence alignment of spidroin C-terminal domains.
FIG. 3 shows electrophoresis gels of fusion proteins.
FIG. 4 shows an electrophoresis gel of a SP-C33Leu protein obtained from a fusion protein.
FIG. 5 shows in vitro surface activity of surfactant suspensions comprising SP-C33Leu obtained from a fusion protein.
FIG. 6 shows electrophoresis gels of SP-C33Leu fusion proteins.
FIG. 7 shows an electrophoresis gel of a Brichos fusion protein.
FIG. 8 shows an electrophoresis gel of a GFP fusion protein and GFP obtained from the fusion protein.
FIG. 9 shows an electrophoresis gel of a neuroserpin fusion protein and neuroserpin obtained from the fusion protein.



DETAILED DESCRIPTION OF THE INVENTION
The present invention is concerned with production proteins and polypeptides, and in particular non-spidroin proteins and polypeptides. Depending on the purpose with this production, the end product may vary. It may for instance be desirable to obtain the protein or polypeptide inserted in a lipid membrane, in solution or associated with other biomolecules. It shall also be realized that it may also be highly desirable to obtain the desired protein or polypeptide as part of a fusion protein, which may provide a suitable handle for purification and detection and/or provide desirable properties, e.g. stability and solubility.
The present invention is generally based on the insight of the usefulness of the N-terminal (NT) fragment of a spider silk protein as a solubility-enhancing moiety in a fusion protein that is produced from recombinant DNA. Thus, the present invention provides according to a first aspect a fusion protein comprising (i) at least one solubility-enhancing moiety which is derived from the NT fragment of a spider silk protein; and (ii) at least one moiety which is a desired protein or polypeptide. In a preferred embodiment, the fusion proteins consists of (i) at least one solubility-enhancing moiety which is derived from the NT fragment of a spider silk protein; and (ii) at least one moiety which is a desired protein or polypeptide, optionally including other preferred features disclosed herein, e.g. a linker peptide and/or a cleavage site between the solubility-enhancing moiety and the desired protein or polypeptide. In experiments, surprisingly high yields of different fusion proteins has been achieved in E. coli. The fusion protein may be useful as such in isolated form, e.g. for studies of otherwise aggregated or poorly soluble proteins in soluble form, or in crystallization associated with X-ray crystallography. The fusion protein may also be cleaved to release the desired protein.
The term “fusion protein” implies here a protein that is made by expression from a recombinant nucleic acid, i.e. DNA or RNA that is created artificially by combining two or more nucleic acid sequences that would not normally occur together (genetic engineering). The fusion proteins according to the invention are recombinant proteins, and they are therefore not identical to naturally occurring proteins. In particular, wildtype spidroins are not fusion proteins according to the invention, because they are not expressed from a recombinant nucleic acid as set out above. The combined nucleic acid sequences encode different proteins, partial proteins or polypeptides with certain functional properties. The resulting fusion protein, or recombinant fusion protein, is a single protein with functional properties derived from each of the original proteins, partial proteins or polypeptides.
In certain embodiments, the fusion protein according to the invention and the corresponding genes are chimeric, i.e. the protein/gene fragments are derived from at least two different species. The solubility-enhancing moiety is derived from the N-terminal fragment of a spider silk protein. According to this aspect, it is preferred that, the desired protein or polypeptide is a non-spidroin protein. This implies that the desired protein or polypeptide is not derived from the C-terminal, repetitive or N-terminal fragment of a spider silk protein.
The fusion protein according to the invention may also contain one or more linker peptides. The linker peptide(s) may be arranged between the solubility-enhancing moiety and the desired protein or polypeptide moiety, or may be arranged at either end of the solubility-enhancing moiety and the desired protein or polypeptide moiety. If the fusion protein contains two or more solubility-enhancing moieties, the linker peptide(s) may also be arranged in between two solubility-enhancing moieties. The linker(s) may provide a spacer between the functional units of the fusion protein, but may also constitute a handle for identification and purification of the fusion protein, e.g. a His and/or a Trx tag. If the fusion protein contains two or more linker peptides for identification and purification of the fusion protein, it is preferred that they are separated by a spacer sequence, e.g. His6-spacer-His6-. The linker may also constitute a signal peptide, such as a signal recognition particle, which directs the fusion protein to the membrane and/or causes secretion of the fusion protein from the host cell into the surrounding medium. The fusion protein may also include a cleavage site in its amino acid sequence, which allows for cleavage and removal of the linker(s) and/or the solubility-enhancing moiety or moieties. Various cleavage sites are known to the person skilled in the art, e.g. cleavage sites for chemical agents, such as CNBr after Met residues and hydroxylamine between Asn-Gly residues, cleavage sites for proteases, such as thrombin or protease 3C. and self-splicing sequences, such as intein self-splicing sequences.
Each solubility-enhancing moiety is linked directly or indirectly to the desired protein or polypeptide moiety. A direct linkage implies a direct covalent binding between the two moieties without intervening sequences, such as linkers. An indirect linkage also implies that the two moieties are linked by covalent bonds, but that there are intervening sequences, such as linkers and/or one or more further solubility-enhancing moieties.
The at least one solubility-enhancing moiety may be arranged at either end of the desired protein or polypeptide, i.e. C-terminally arranged or N-terminally arranged. It is preferred that the least one solubility-enhancing moiety is arranged at the N-terminal end of the desired protein or polypeptide. If the fusion protein contains one or more linker peptide(s) for identification and purification of the fusion protein, e.g. a His or Trx tag(s), it is preferred that it is arranged at the N-terminal end of the fusion protein. The at least one solubility-enhancing moiety may also be integrated within the desired protein or polypeptide, for instance between domains or parts of a desired protein. In a preferred embodiment, at least one solubility-enhancing moiety constitutes the N-terminal and/or the C-terminal end of the fusion protein, i.e. no linker peptide or other sequence is present terminal of the solubility-enhancing moiety. A typical fusion protein according to the invention may contain 1-6, such as 1-4, such as 1-2 solubility-enhancing moieties.
In a preferred embodiment, the fusion protein is comprising at least two solubility-enhancing moieties, each being derived from the N-terminal (NT) fragment of a spider silk protein. The solubility-enhancing moieties, preferably two solubility-enhancing moieties, may be consecutively arranged at either end of the desired protein or polypeptide, i.e. C-terminally arranged or N-terminally arranged. Consecutively arranged solubility-enhancing moieties may also be integrated within the desired protein or polypeptide, for instance between domains or parts of a desired protein. The solubility-enhancing moieties may also be non-consecutively arranged, either at each end of the desired protein or polypeptide, i.e. C-terminally and N-terminally arranged, or at one end of the desired protein or polypeptide and integrated within the desired protein or polypeptide. A typical preferred fusion protein according to the invention may contain 2-6, such as 2-4 solubility-enhancing moieties.
In a preferred embodiment, the fusion protein according has at least one cleavage site arranged between at least one desired protein or polypeptide moiety and at least one solubility-enhancing moiety. This allows for cleavage of the fusion protein and purification of the desired protein. It is however noted that it may be desirable to obtain the desired protein or polypeptide as part of a fusion protein, which may provide a suitable handle for purification and detection and/or provide desirable properties, e.g. stability and solubility. In this case, the cleavage site may be omitted, or the cleavage site may be included but the cleavage step omitted.
A preferred fusion protein has the form of an N-terminally arranged solubility-enhancing moiety, coupled by a linker peptide of 1-30 amino acid residues, such as 1-10 amino acid residues, to a C-terminally arranged desired protein or polypeptide. The linker peptide may contain a cleavage site. Optionally, the fusion protein has an N-terminal or C-terminal linker peptide, which may contain a purification tag, such as a His tag, and a cleavage site.
Another preferred fusion protein has the form of an N-terminally arranged solubility-enhancing moiety coupled directly to a C-terminally arranged desired protein or polypeptide. Optionally, the fusion protein has an N-terminal or C-terminal linker peptide, which may contain a purification tag, such as a His tag, and a cleavage site.
One preferred fusion protein has the form of a two consecutive N-terminally arranged solubility-enhancing moieties, coupled by a linker peptide of 1-30 amino acid residues, such as 1-10 amino acid residues, to a C-terminally arranged desired protein or polypeptide. The linker peptide may contain a cleavage site. Optionally, the fusion protein has an N-terminal or C-terminal linker peptide, which may contain a purification tag, such as a His tag, and a cleavage site.
Another preferred fusion protein has the form of two consecutive N-terminally arranged solubility-enhancing moieties coupled directly to a C-terminally arranged desired protein or polypeptide. Optionally, the fusion protein has an N-terminal or C-terminal linker peptide, which may contain a purification tag, such as a His tag, and a cleavage site.
The solubility-enhancing moiety is derived from the NT fragment of a spider silk protein, or spidroin. Although the examples by necessity relate to specific NT fragments, in this case proteins derived from major spidroin 1 (MaSp1) from Euprosthenops australis, it is considered that the method disclosed herein is applicable to any similar protein moiety. The terms “spidroins” and “spider silk proteins” are used interchangeably throughout the description and encompass all known spider silk proteins, including major ampullate spider silk proteins which typically are abbreviated “MaSp”, or “ADF” in the case of Araneus diadematus. These major ampullate spider silk proteins are generally of two types, 1 and 2. These terms furthermore include the new NT protein fragments according to the invention, as defined in the appended claims and itemized embodiments, and other non-natural proteins with a high degree of identity and/or similarity to the known spider silk NT protein fragments.
The solubility-enhancing moiety has a high degree of similarity to the N-terminal (NT) amino acid sequence of spider silk proteins. As shown in FIG. 1, this amino acid sequence is well conserved among various species and spider silk proteins, including MaSp1 and MaSp2. In FIG. 1, the following spidroin NT fragments are aligned, denoted with GenBank accession entries where applicable:







TABLE 1







Spidroin NT fragments











GenBank


Code
Species and spidroin protein
acc. no.





Ea MaSp1
Euprosthenops australis MaSp 1
AM259067


Lg MaSp1
Latrodectus geometricus MaSp 1
ABY67420


Lh MaSp1
Latrodectus hesperus MaSp 1
ABY67414


Nc MaSp1
Nephila clavipes MaSp 1
ACF19411


At MaSp2
Argiope trifasciata MaSp 2
AAZ15371


Lg MaSp2
Latrodectus geometricus MaSp 2
ABY67417


Lh MaSp2
Latrodectus hesperus MaSp 2
ABR68855


Nim MaSp2
Nephila inaurata madagascariensis MaSp 2
AAZ15322


Nc MaSp2
Nephila clavipes MaSp 2
ACF19413


Ab CySp1
Argiope bruennichi cylindriform spidroin 1
BAE86855


Ncl CySp1
Nephila clavata cylindriform spidroin 1
BAE54451


Lh TuSp1
Latrodectus hesperus tubuliform spidroin
ABD24296


Nc Flag
Nephila clavipes flagelliform silk protein
AF027972


Nim Flag
Nephila inaurata madagascariensis
AF218623



flagelliform silk protein
(translated)









Only the part corresponding to the N-terminal domain is shown for each sequence, omitting the signal peptide. Nc flag and Nlm flag are translated and edited according to Rising A. et al. Biomacromolecules 7, 3120-3124 (2006)).
It is not critical which specific solubility-enhancing moiety is present in fusion proteins according to the invention, as long as the solubility-enhancing moiety is not entirely missing. Thus, the solubility-enhancing moiety according to the invention can be selected from any of the amino acid sequences shown in FIG. 1 or sequences with a high degree of similarity. A wide variety of solubility-enhancing sequences can be used in the fusion protein according to the invention. Based on the homologous sequences of FIG. 1, the following sequence constitutes a consensus solubility-enhancing amino acid sequence:







(SEQ ID NO 8)


QANTPWSSPNLADAFINSF(M/L)SA(A/I)SSSGAFSADQLDDMSTI


 


G(D/N/Q)TLMSAMD(N/S/K)MGRSG(K/R)STKSKLQALNMAFASS


 


MAEIAAAESGG(G/Q)SVGVKTNAISDALSSAFYQTTGSVNPQFV


 


(N/S)EIRSLI(G/N)M(F/L)(A/S)QASANEV.






The sequence of the solubility-enhancing moiety according to the invention has at least 50% identity, preferably at least 60% identity, to the consensus amino acid sequence SEQ ID NO 8, which is based on the amino acid sequences of FIG. 1. In a preferred embodiment, the sequence of the solubility-enhancing moiety according to the invention has at least 65% identity, preferably at least 70% identity, to the consensus amino acid sequence SEQ ID NO 8. In preferred embodiments, the solubility-enhancing moiety according to the invention has furthermore 70%, preferably 80%, similarity to the consensus amino acid sequence SEQ ID NO 8.
A representative solubility-enhancing moiety according to the invention is the Euprosthenops australis sequence SEQ ID NO 6. According to a preferred embodiment of the invention, the solubility-enhancing moiety has at least 80% identity to SEQ ID NO 6 or any individual amino acid sequence in FIG. 1. In preferred embodiments of the invention, the solubility-enhancing moiety has at least 90%, such as at least 95% identity, to SEQ ID NO 6 or any individual amino acid sequence in FIG. 1. In preferred embodiments of the invention, the solubility-enhancing moiety is identical to SEQ ID NO 6 or any individual amino acid sequence in FIG. 1, in particular to Ea MaSp1.
The term “% identity”, as used throughout the specification and the appended claims, is calculated as follows. The query sequence is aligned to the target sequence using the CLUSTAL W algorithm (Thompson, J. D., Higgins, D. G. and Gibson, T. J., Nucleic Acids Research, 22: 4673-4680 (1994)). A comparison is made over the window corresponding to the shortest of the aligned sequences. The amino acid residues at each position are compared, and the percentage of positions in the query sequence that have identical correspondences in the target sequence is reported as % identity.
The term “% similarity”, as used throughout the specification and the appended claims, is calculated as described for “% identity”, with the exception that the hydrophobic residues Ala, Val, Phe, Pro, Leu, Ile, Trp, Met and Cys are similar; the basic residues Lys, Arg and His are similar; the acidic residues Glu and Asp are similar; and the hydrophilic, uncharged residues Gln, Asn, Ser, Thr and Tyr are similar. The remaining natural amino acid Gly is not similar to any other amino acid in this context.
Throughout this description, alternative embodiments according to the invention fulfill, instead of the specified percentage of identity, the corresponding percentage of similarity. Other alternative embodiments fulfill the specified percentage of identity as well as another, higher percentage of similarity, selected from the group of preferred percentages of identity for each sequence. For example, a sequence may be 70% similar to another sequence; or it may be 70% identical to another sequence; or it may be 70% identical and 90% similar to another sequence.
The solubility-enhancing moiety contains from 100 to 160 amino acid residues. It is preferred that the solubility-enhancing moiety contains at least 100, or more than 110, preferably more than 120, amino acid residues. It is also preferred that the solubility-enhancing moiety contains at most 160, or less than 140 amino acid residues. A typical solubility-enhancing moiety contains approximately 130-140 amino acid residues.
In certain embodiments of the present invention, the desired protein or polypeptide is a spidroin protein or polypeptide. The sequence of a desired spidroin protein or polypeptide according to the invention has at least 50% identity, such as at least 60% identity, preferably at least 70% identity, to any of the spidroin amino acid sequences disclosed herein. In a preferred embodiment, the sequence of a desired spidroin protein or polypeptide according to the invention has at least 80% identity, preferably at least 90% identity, to any of the spidroin amino acid sequences disclosed herein.
In a preferred embodiment, the desired spidroin protein is comprising a repetitive fragment of from 70 to 300 amino acid residues derived from the repetitive fragment of a spider silk protein; and a C-terminal fragment of from 70 to 120 amino acid residues, which fragment is derived from the C-terminal fragment of a spider silk protein. Optionally, the desired spidroin protein is comprising an N-terminal fragment of from 100 to 160 amino acid residues derived from the N-terminal fragment of a spider silk protein. The desired spidroin protein consists of from 170 to 600 amino acid residues, preferably from 280 to 600 amino acid residues, such as from 300 to 400 amino acid residues, more preferably from 340 to 380 amino acid residues. The small size is advantageous because longer spider silk proteins tend to form amorphous aggregates, which require use of harsh solvents for solubilisation and polymerisation. The protein fragments are covalently coupled, typically via a peptide bond.
In specific preferred embodiments, the desired spidroin protein is selected from the group of proteins defined by the formulas NT2-REP-CT (or NT-NT-REP-CT), NT-REP-CT and REP-CT.
The NT fragment has a high degree of similarity to the N-terminal amino acid sequence of spider silk proteins. As shown in FIG. 1, this amino acid sequence is well conserved among various species and spider silk proteins, including MaSp1 and MaSp2, see also Table 1:
It is not critical which specific NT fragment is present in desired spidroin proteins according to the invention. Thus, the NT fragment according to the invention can be selected from any of the amino acid sequences shown in FIG. 1 or sequences with a high degree of similarity. A wide variety of N-terminal sequences can be used in the desired spidroin protein according to the invention. Based on the homologous sequences of FIG. 1, the following sequence constitutes a consensus NT amino acid sequence:







(SEQ ID NO: 8)


QANTPWSSPNLADAFINSF(M/L)SA(A/I)SSSGAFSADQLDDMSTI


 


G(D/N/Q)TLMSAMD(N/S/K)MGRSG(K/R)STKSKLQALNMAFASS


 


MAEIAAAESGG(G/Q)SVGVKTNAISDALSSAFYQTTGSVNPQFV


 


(N/S)EIRSLI(G/N)M(F/L)(A/S)QASANEV.






The sequence of the NT fragment according to the invention has at least 50% identity, preferably at least 60% identity, to the consensus amino acid sequence SEQ ID NO: 8, which is based on the amino acid sequences of FIG. 1. In a preferred embodiment, the sequence of the NT fragment according to the invention has at least 65% identity, preferably at least 70% identity, to the consensus amino acid sequence SEQ ID NO: 8. In preferred embodiments, the NT fragment according to the invention has furthermore 70%, preferably 80%, similarity to the consensus amino acid sequence SEQ ID NO: 8.
A representative NT fragment according to the invention is the Euprosthenops australis sequence SEQ ID NO: 6. According to a preferred embodiment of the invention, the NT fragment has at least 80% identity to SEQ ID NO: 6 or any individual amino acid sequence in FIG. 1. In preferred embodiments of the invention, the NT fragment has at least 90%, such as at least 95% identity, to SEQ ID NO: 6 or any individual amino acid sequence in FIG. 1. In preferred embodiments of the invention, the NT fragment is identical to SEQ ID NO: 6 or any individual amino acid sequence in FIG. 1, in particular to Ea MaSp1.
The NT fragment contains from 100 to 160 amino acid residues. It is preferred that the NT fragment contains at least 100, or more than 110, preferably more than 120, amino acid residues. It is also preferred that the NT fragment contains at most 160, or less than 140 amino acid residues. A typical NT fragment contains approximately 130-140 amino acid residues.
The REP fragment has a repetitive character, alternating between alanine-rich stretches and glycine-rich stretches. The REP fragment generally contains more than 70, such as more than 140, and less than 300, preferably less than 240, such as less than 200, amino acid residues, and can itself be divided into several L (linker) segments, A (alanine-rich) segments and G (glycine-rich) segments, as will be explained in more detail below. Typically, said linker segments, which are optional, are located at the REP fragment terminals, while the remaining segments are in turn alanine-rich and glycine-rich. Thus, the REP fragment can generally have either of the following structures, wherein n is an integer:

    L(AG)nL, such as LA1G1A2G2A3G3A4G4A5G5L;
    L(AG)nAL, such as LA1G1A2G2A3G3A4G4A5G5A6L;
    L(GA)nL, such as LG1A1G2A2G3A3G4A4G5A5L; or
    L(GA)nGL, such as LG1A1G2A2G3A3G4A4G5A5G6L.

It follows that it is not critical whether an alanine-rich or a glycine-rich segment is adjacent to the N-terminal or C-terminal linker segments. It is preferred that n is an integer from 2 to 10, preferably from 2 to 8, also preferably from 4 to 8, more preferred from 4 to 6, i.e. n=4, n=5 or n=6.



In preferred embodiments, the alanine content of the REP fragment according to the invention is above 20%, preferably above 25%, more preferably above 30%, and below 50%, preferably below 40%, more preferably below 35%. This is advantageous, since it is contemplated that a higher alanine content provides a stiffer and/or stronger and/or less extendible fiber.
In certain embodiments, the REP fragment is void of proline residues, i.e. there are no Pro residues in the REP fragment.
Now turning to the segments that constitute the REP fragment according to the invention, it shall be emphasized that each segment is individual, i.e. any two A segments, any two G segments or any two L segments of a specific REP fragment may be identical or may not be identical. Thus, it is not a general feature of the invention that each type of segment is identical within a specific REP fragment. Rather, the following disclosure provides the skilled person with guidelines how to design individual segments and gather them into a REP fragment, which is a part of a functional spider silk protein according to the invention.
Each individual A segment is an amino acid sequence having from 8 to 18 amino acid residues. It is preferred that each individual A segment contains from 13 to 15 amino acid residues. It is also possible that a majority, or more than two, of the A segments contain from 13 to 15 amino acid residues, and that a minority, such as one or two, of the A segments contain from 8 to 18 amino acid residues, such as 8-12 or 16-18 amino acid residues. A vast majority of these amino acid residues are alanine residues. More specifically, from 0 to 3 of the amino acid residues are not alanine residues, and the remaining amino acid residues are alanine residues. Thus, all amino acid residues in each individual A segment are alanine residues, with no exception or the exception of one, two or three amino acid residues, which can be any amino acid. It is preferred that the alanine-replacing amino acid(s) is (are) natural amino acids, preferably individually selected from the group of serine, glutamic acid, cysteine and glycine, more preferably serine. Of course, it is possible that one or more of the A segments are all-alanine segments, while the remaining A segments contain 1-3 non-alanine residues, such as serine, glutamic acid, cysteine or glycine.
In a preferred embodiment, each A segment contains 13-15 amino acid residues, including 10-15 alanine residues and 0-3 non-alanine residues as described above. In a more preferred embodiment, each A segment contains 13-15 amino acid residues, including 12-15 alanine residues and 0-1 non-alanine residues as described above.
It is preferred that each individual A segment has at least 80%, preferably at least 90%, more preferably 95%, most preferably 100% identity to an amino acid sequence selected from the group of amino acid residues 7-19, 43-56, 71-83, 107-120, 135-147, 171-183, 198-211, 235-248, 266-279, 294-306, 330-342, 357-370, 394-406, 421-434, 458-470, 489-502, 517-529, 553-566, 581-594, 618-630, 648-661, 676-688, 712-725, 740-752, 776-789, 804-816, 840-853, 868-880, 904-917, 932-945, 969-981, 999-1013, 1028-1042 and 1060-1073 of SEQ ID NO: 10. Each sequence of this group corresponds to a segment of the naturally occurring sequence of Euprosthenops australis MaSp1 protein, which is deduced from cloning of the corresponding cDNA, see WO 2007/078239. Alternatively, each individual A segment has at least 80%, preferably at least 90%, more preferably 95%, most preferably 100% identity to an amino acid sequence selected from the group of amino acid residues 143-152, 174-186, 204-218, 233-247 and 265-278 of SEQ ID NO: 3. Each sequence of this group corresponds to a segment of expressed, non-natural spider silk proteins according to the invention, which proteins have capacity to form silk fibers under appropriate conditions. Thus, in certain embodiments according to the invention, each individual A segment is identical to an amino acid sequence selected from the above-mentioned amino acid segments. Without wishing to be bound by any particular theory, it is envisaged that A segments according to the invention form helical structures or beta sheets.
Furthermore, it has been concluded from experimental data that each individual G segment is an amino acid sequence of from 12 to 30 amino acid residues. It is preferred that each individual G segment consists of from 14 to 23 amino acid residues. At least 40% of the amino acid residues of each G segment are glycine residues. Typically the glycine content of each individual G segment is in the range of 40-60%.
It is preferred that each individual G segment has at least 80%, preferably at least 90%, more preferably 95%, most preferably 100% identity to an amino acid sequence selected from the group of amino acid residues 20-42, 57-70, 84-106, 121-134, 148-170, 184-197, 212-234, 249-265, 280-293, 307-329, 343-356, 371-393, 407-420, 435-457, 471-488, 503-516, 530-552, 567-580, 595-617, 631-647, 662-675, 689-711, 726-739, 753-775, 790-803, 817-839, 854-867, 881-903, 918-931, 946-968, 982-998, 1014-1027, 1043-1059 and 1074-1092 of SEQ ID NO: 10. Each sequence of this group corresponds to a segment of the naturally occurring sequence of Euprosthenops australis MaSp1 protein, which is deduced from cloning of the corresponding cDNA, see WO 2007/078239. Alternatively, each individual G segment has at least 80%, preferably at least 90%, more preferably 95%, most preferably 100% identity to an amino acid sequence selected from the group of amino acid residues 153-173, 187-203, 219-232, 248-264 and 279-296 of SEQ ID NO: 3. Each sequence of this group corresponds to a segment of expressed, non-natural spider silk proteins according to the invention, which proteins have capacity to form silk fibers under appropriate conditions. Thus, in certain embodiments according to the invention, each individual G segment is identical to an amino acid sequence selected from the above-mentioned amino acid segments.
In certain embodiments, the first two amino acid residues of each G segment according to the invention are not -Gln-Gln-.
There are the three subtypes of the G segment according to the invention. This classification is based upon careful analysis of the Euprosthenops australis MaSp1 protein sequence (WO 2007/078239), and the information has been employed and verified in the construction of novel, non-natural spider silk proteins.
The first subtype of the G segment according to the invention is represented by the amino acid one letter consensus sequence GQG(G/S)QGG(Q/Y)GG (L/Q)GQGGYGQGA GSS (SEQ ID NO: 11). This first, and generally the longest, G segment subtype typically contains 23 amino acid residues, but may contain as little as 17 amino acid residues, and lacks charged residues or contain one charged residue. Thus, it is preferred that this first G segment subtype contains 17-23 amino acid residues, but it is contemplated that it may contain as few as 12 or as many as 30 amino acid residues. Without wishing to be bound by any particular theory, it is envisaged that this subtype forms coil structures or 31-helix structures. Representative G segments of this first subtype are amino acid residues 20-42, 84-106, 148-170, 212-234, 307-329, 371-393, 435-457, 530-552, 595-617, 689-711, 753-775, 817-839, 881-903, 946-968, 1043-1059 and 1074-1092 of SEQ ID NO: 10. In certain embodiments, the first two amino acid residues of each G segment of this first subtype according to the invention are not -Gln-Gln-.
The second subtype of the G segment according to the invention is represented by the amino acid one letter consensus sequence GQGGQGQG(G/R)Y GQG(A/S)G(S/G)S (SEQ ID NO: 12). This second, generally mid-sized, G segment subtype typically contains 17 amino acid residues and lacks charged residues or contain one charged residue. It is preferred that this second G segment subtype contains 14-20 amino acid residues, but it is contemplated that it may contain as few as 12 or as many as 30 amino acid residues. Without wishing to be bound by any particular theory, it is envisaged that this subtype forms coil structures. Representative G segments of this second subtype are amino acid residues 249-265, 471-488, 631-647 and 982-998 of SEQ ID NO: 10; and amino acid residues 187-203 of SEQ ID NO: 3.
The third subtype of the G segment according to the invention is represented by the amino acid one letter consensus sequence G(R/Q)GQG(G/R)YGQG (A/S/V)GGN (SEQ ID NO: 13). This third G segment subtype typically contains 14 amino acid residues, and is generally the shortest of the G segment subtypes according to the invention. It is preferred that this third G segment subtype contains 12-17 amino acid residues, but it is contemplated that it may contain as many as 23 amino acid residues. Without wishing to be bound by any particular theory, it is envisaged that this subtype forms turn structures. Representative G segments of this third subtype are amino acid residues 57-70, 121-134, 184-197, 280-293, 343-356, 407-420, 503-516, 567-580, 662-675, 726-739, 790-803, 854-867, 918-931, 1014-1027 of SEQ ID NO: 10; and amino acid residues 219-232 of SEQ ID NO: 3.
Thus, in preferred embodiments, each individual G segment has at least 80%, preferably 90%, more preferably 95%, identity to an amino acid sequence selected from SEQ ID NO: 11, SEQ ID NO: 12 and SEQ ID NO: 13.
In a preferred embodiment of the alternating sequence of A and G segments of the REP fragment, every second G segment is of the first subtype, while the remaining G segments are of the third subtype, e.g. . . . A1GshortA2GlongA3GshortA4GlongA5Gshort . . . . In another preferred embodiment of the REP fragment, one G segment of the second subtype interrupts the G segment regularity via an insertion, e.g. . . . A1GshortA2GlongA3GmidA4GshortA5Glong . . . .
Each individual L segment represents an optional linker amino acid sequence, which may contain from 0 to 20 amino acid residues, such as from 0 to 10 amino acid residues. While this segment is optional and not functionally critical for the spider silk protein, its presence still allows for fully functional spider silk proteins, forming spider silk fibers according to the invention. There are also linker amino acid sequences present in the repetitive part (SEQ ID NO: 10) of the deduced amino acid sequence of the MaSp1 protein from Euprosthenops australis. In particular, the amino acid sequence of a linker segment may resemble any of the described A or G segments, but usually not sufficiently to meet their criteria as defined herein.
As shown in WO 2007/078239, a linker segment arranged at the C-terminal part of the REP fragment can be represented by the amino acid one letter consensus sequences ASASAAASAA STVANSVS (SEQ ID NO: 64) and ASAASAAA (SEQ ID NO: 65), which are rich in alanine. In fact, the second sequence can be considered to be an A segment according to the invention, while the first sequence has a high degree of similarity to A segments according to the invention. Another example of a linker segment according the invention has the one letter amino acid sequence GSAMGQGS (SEQ ID NO: 66), which is rich in glycine and has a high degree of similarity to G segments according to the invention. Another example of a linker segment is SASAG (SEQ ID NO: 67).
Representative L segments are amino acid residues 1-6 and 1093-1110 of SEQ ID NO: 10; and amino acid residues 138-142 of SEQ ID NO: 3, but the skilled person in the art will readily recognize that there are many suitable alternative amino acid sequences for these segments. In one embodiment of the REP fragment according to the invention, one of the L segments contains 0 amino acids, i.e. one of the L segments is void. In another embodiment of the REP fragment according to the invention, both L segments contain 0 amino acids, i.e. both L segments are void. Thus, these embodiments of the REP fragments according to the invention may be schematically represented as follows: (AG)nL, (AG)nAL, (GA)nL, (GA)nGL; L(AG)n, L(AG)nA, L(GA)n, L(GA)nG; and (AG)n, (AG)nA, (GA)n, (GA)nG. Any of these REP fragments are suitable for use with any CT fragment as defined below.
The CT fragment of the desired spidroin protein has a high degree of similarity to the C-terminal amino acid sequence of spider silk proteins. As shown in WO 2007/078239, this amino acid sequence is well conserved among various species and spider silk proteins, including MaSp1 and MaSp2. A consensus sequence of the C-terminal regions of MaSp1 and MaSp2 is provided as SEQ ID NO: 9. In FIG. 2, the following MaSp proteins are aligned, denoted with GenBank accession entries where applicable:







TABLE 2







Spidroin CT fragments










Species and spidroin protein
Entry







Euprosthenops sp MaSp1
Cthyb_Esp



(Pouchkina-Stantcheva, N N &



McQueen-Mason, S J, ibid)



Euprosthenops australis MaSp1
CTnat_Eau



Argiope trifasciata MaSp1
AF350266_At1



Cyrtophora moluccensis Sp1
AY666062_Cm1



Latrodectus geometricus MaSp1
AF350273_Lg1



Latrodectus hesperus MaSp1
AY953074_Lh1



Macrothele holsti Sp1
AY666068_Mh1



Nephila clavipes MaSp1
U20329_Nc1



Nephila pilipes MaSp1
AY666076_Np1



Nephila madagascariensis MaSp1
AF350277_Nm1



Nephila senegalensis MaSp1
AF350279_Ns1



Octonoba varians Sp1
AY666057_Ov1



Psechrus sinensis Sp1
AY666064_Ps1



Tetragnatha kauaiensis MaSp1
AF350285_Tk1



Tetragnatha versicolor MaSp1
AF350286_Tv1



Araneus bicentenarius Sp2
ABU20328_Ab2



Argiope amoena MaSp2
AY365016_Aam2



Argiope aurantia MaSp2
AF350263_Aau2



Argiope trifasciata MaSp2
AF350267_At2



Gasteracantha mammosa MaSp2
AF350272_Gm2



Latrodectus geometricus MaSp2
AF350275_Lg2



Latrodectus hesperus MaSp2
AY953075_Lh2



Nephila clavipes MaSp2
AY654293_Nc2



Nephila madagascariensis MaSp2
AF350278_Nm2



Nephila senegalensis MaSp2
AF350280_Ns2



Dolomedes tenebrosus Fb1
AF350269_DtFb1



Dolomedes tenebrosus Fb2
AF350270_DtFb2



Araneus diadematus ADF-1
U47853_ADF1



Araneus diadematus ADF-2
U47854_ADF2



Araneus diadematus ADF-3
U47855_ADF3



Araneus diadematus ADF-4
U47856_ADF4










It is not critical which specific CT fragment, if any, is present in spider silk proteins according to the invention. Thus, the CT fragment according to the invention can be selected from any of the amino acid sequences shown in FIG. 2 and Table 2 or sequences with a high degree of similarity. A wide variety of C-terminal sequences can be used in the spider silk protein according to the invention.
The sequence of the CT fragment according to the invention has at least 50% identity, preferably at least 60%, more preferably at least 65% identity, or even at least 70% identity, to the consensus amino acid sequence SEQ ID NO: 9, which is based on the amino acid sequences of FIG. 2.
A representative CT fragment according to the invention is the Euprosthenops australis sequence SEQ ID NO: 7, Thus, according to a preferred aspect of the invention, the CT fragment has at least 80%, preferably at least 90%, such as at least 95%, identity to SEQ ID NO: 7 or any individual amino acid sequence of FIG. 2 and Table 2. In preferred aspects of the invention, the CT fragment is identical to SEQ ID NO: 7 or any individual amino acid sequence of FIG. 2 and Table 2.
The CT fragment typically consists of from 70 to 120 amino acid residues. It is preferred that the CT fragment contains at least 70, or more than 80, preferably more than 90, amino acid residues. It is also preferred that the CT fragment contains at most 120, or less than 110 amino acid residues. A typical CT fragment contains approximately 100 amino acid residues.
According to another aspect, the desired protein or polypeptide according to the invention is a non-spidroin protein or polypeptide when the fusion protein comprises a single solubility-enhancing moiety which is derived from the N-terminal (NT) fragment of a spider silk protein. In a preferred embodiment, the desired protein or polypeptide is a non-spidroin protein or polypeptide. The sequence of a desired non-spidroin protein or polypeptide according to the invention preferably has less than 30% identity, such as less than 20% identity, preferably less than 10% identity, to any of the spidroin amino acid sequences disclosed herein, and specifically to any of SEQ ID NO: 6-10.
In a preferred embodiment, the desired non-spidroin protein or polypeptide is derived from sponges, comb jellies, jellyfishes, corals, anemones, flatworms, rotifers, roundworms, ribbon worms, clams, snails, octopuses, segmented worms, crustaceans, insects, bryozoans, brachiopods, phoronids, sea stars, sea urchins, tunicates, lancelets, vertebrates, including human, plants, fungi, yeast, bacteria, archaebacteria or viruses or is an artificial protein or polypeptide. By “derived” is meant that the sequence of a desired non-spidroin protein or polypeptide according to the invention has preferably at least 50% identity, preferably at least 60%, preferably at least 70%, more preferably at least 80% identity, or even at least 90% identity, such as 95-100% identity, to a corresponding naturally occurring protein and having a maintained function. In one preferred embodiment, the desired non-spidroin protein or polypeptide is derived from molluscs, insects, vertebrates, including human, plants, fungi, yeast, bacteria, archaebacteria or viruses or is an artificial protein or polypeptide. In a preferred embodiment, the desired non-spidroin protein or polypeptide is derived from vertebrates, including human, plants, fungi, yeast, bacteria, archaebacteria or viruses or is an artificial protein or polypeptide.
In a preferred embodiment, the desired non-spidroin protein or polypeptide is selected from the group consisting of amyloid-forming proteins and polypeptides, disulphide-containing proteins and polypeptides, apolipoproteins, membrane proteins and polypeptides, protein and polypeptide drugs and drug targets, aggregation-prone proteins and polypeptides, and proteases.
Amyloid-forming proteins and polypeptides according to the invention include proteins and polypeptides that are associated with disease and functional amyloid. Examples of amyloid-forming proteins and polypeptides include amyloid beta peptide (Aβ-peptide), islet amyloid polypeptide (amylin or IAPP), prion protein (PrP), α-synuclein, calcitonin, prolactin, cystatin, atrial natriuretic factor (ATF) and actin. Examples of amyloid-forming proteins and polypeptides according to the invention are listed in Table 3.







TABLE 3







Amyloid-forming proteins and polypeptides










Protein
Uniprot ID







Aβ1-42
P05067



Apolipoprotein SAA
P02735



Cystatin C
P01034



Transthyretin
P02766



Lysozyme
P61626



α-synuclein
P37840



Prion protein
P04156



ODAM
A1E959



Lactadherin
Q08431



Tau
P10636



Gelsolin
P06396



ABri, ADan
Q9Y287



Insulin
P01308



Apolipoprotein A-II
P02652



Apolipoprotein A-IV
P06727



Semenogelin I
P04279



Keratoepithelin
Q15582



Lactotransferrin
P02788



Fibrinogen α-chain
P02671



ANF
P01160



IAPP
P10997



β2-microglobulin
P61769



Calcitonin
P01258



Prolactin
P01236



Apolipoprotein A-I
P02647



CsgA
P28307



Sup35
C7GN25



Pmel17
P40967



HET-s
A8HR89



Ure2p
Q8NIE6










Examples of disulphide-containing proteins and polypeptides include surfactant protein B (SP-B) and variants thereof, such as Mini-B, Mini-B27, Mini-BLeu, α-defensins and β-defensins. Without being limited to any specific theory, it is contemplated that the solubility-enhancing moiety promotes the desired formation of intrachain disulphide bonds over interchain disulphide bonds in defensins and other disulphide-containing proteins and polypeptides. Examples of disulphide-containing proteins and polypeptides according to the invention are listed in Table 4.







TABLE 4







Disulphide-containinq proteins and polypeptides








Protein
Sequence/Uniprot ID





Human
FPIPLPYCWLCRALIKRIQAMIPKGALAVAVAQVCRVVPL


SP-B
VAGGICQCLAERYSVILLDTLLGRMLPQLVCRLVLRCSM a


 


Mouse
LPIPLPFCWLCRTLIKRVQAVIPKGVLAVAVSQVCHVVPL


SP-B
VVGGICQCLAERYTVLLLDALLGRVVPQLVCGLVLRCST a


 


Pig
FPIPLPFCWLCRTLIKRIQAVVPKGVLLKAVAQVCHVVPL


SP-B
PVGGICQCLAERYIVICLNMLLDRTLPQLVCGLVLRCSS a


 


Rabbit
FPIPLPLCWLCRTLLKRIQAMIPKGVLAMAVAQVCHVVPL


SP-B
VVGGICQCLAERYTVILLEVLLGHVLPQLVCGLVLRCSS a


 


Rat
LPIPLPFCWLCRTLIKRVQAVIPKGVLAVAVSQVCHVVPL


SP-B
VVGGICQCLAERYTVLLLDALLGRVVPQLVCGLVLRCST a


 


Mini-B
CWLCRALIKRIQAMIPKGGRMLPQLVCRLVLRCS b


 


Mini-
CWLCRALIKRIQALIPKGGRLLPQLVCRLVLRCS b


BLeu



 


Mini-
CLLCRALIKRFNRYLTPQLVCRLVLRC c


B27



 


1a AA
CWLARALIKRIQALIPKGGRLLPQLVARLVLRCS d


 


1b AA
AWLCRALIKRIQALIPKGGRLLPQLVCRLVLRAS e


 


1a LL
CWLLRALIKRIQALIPKGGRLLPQLVLRLVLRCS d


 


1b LL
LWLCRALIKRIQALIPKGGRLLPQLVCRLVLRLS e


 


Proin-
P01308


sulin



 


CAR
P78310


D1 f



 


Brichos
SEQ ID NO: 41





a Cys8-Cys77, Cys11-Cys71, Cys35-Cys46 and intermolecular Cys48-Cys48 linkages


b Cys1-Cys33 and C4-C27 linkages


c Cys1-Cys27 and C4-C21 linkages


d Cys1-Cys33 linkage


e Cys4-Cys27 linkage


f Coxsackievirus and adenovirus receptor






Examples of apolipoproteins include class A-H apolipoproteins. Examples of apolipoproteins according to the invention are listed in Table 5.







TABLE 5







Apolipoproteins










Protein
Sequence/Uniprot ID







Apolipoprotein B-100
P04114



Apolipoprotein C-1
P02654



Apolipoprotein D
P05090



Apolipoprotein E
P02649










Examples of membrane proteins and polypeptides include membrane-associated receptors, including cytokine receptors, KL4, LL-37, surfactant protein C(SP-C) and variants thereof, such as SP-C(Leu), SP-C33, SP-C30 and SP-C33Leu. Other specific examples include SP-C33Leu fused to Mini-B,Mini-BLeu, 1a AA, 1b AA, 0 AAAA, 1a LL, 1b LL, 0 LLLL or SP-B proteins, optionally via a linker, e.g. Glyn, Leun, Gly-Alan or the like. SP-C33Leu may be arranged N-terminal or, preferably, C-terminal to the Mini-B,Mini-BLeu, 1a AA, 1b AA, 0 AAAA, 1a LL, 1b LL, 0 LLLL or SP-B protein. Examples of membrane proteins and polypeptides according to the invention are listed in Table 6.







TABLE 6





Membrane proteins and polypeptides
















Protein
Sequence





SP-C
FGIPCCPVHLKRLLIVVVVVVLIVVVIV



GALLMGL *


 


SP-C(Leu)
FGIPSSPVHLKRLKLLLLLLLLILLLILGALLMGL


 


SP-C33
IPSSPVHLKRLKLLLLLLLLILLLILGALLMGL


 


SP-C30
IPSSPVHLKRLKLLLLLLLLILLLILGALL


 


SP-C33(Leu)
IPSSPVHLKRLKLLLLLLLLILLLILGALLLGL


 


LL-37
LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLV



PRTES


 


KL4
KLLLLKLLLLKLLLLKLLLLK










* Cys-5 and Cys-6 in native SP-C are palmitoylated











Protein
Uniprot ID





Growth hormone receptor
P10912


 


G-protein coupled
Q9HC97


receptor 35



 


Insulin receptor,
P06213


 


Gonadotropin releasing
P30968


hormone receptor



 


Very low density lipoprotein
P98155


receptor



 


TGF-beta receptor, type 1
P36897


 


Prostaglandin D2 receptor
Q13258


 


Receptor tyrosine-protein
P04626


kinase erbB-2 (HER2)



 


Receptor tyrosine-protein
Q15303


kinase erbB-4 (HER4)



 


Receptor tyrosine-protein
P21860


kinase erbB-3 (HER3)



 


Aquaporin-1
P29972


 


Aquaporin-2
P41181


 


Chloride channel protein
P51800


CIC-Ka



 


Chloride channel protein
P51801


CIC-Kb



 


Integral membrane protein
P98153


DGCR2/IDD



 


Interleukin 9 receptor
Q01113









Examples of protein and polypeptide drugs and drug targets include hormones that are produced recombinantly, including peptide and protein hormones, such as erythropoietin (EPO) and growth hormone (GH), cytokines, growth factors, such as insulin-like growth factors (IGF-I and IGF-II), KL4, LL-37, surfactant protein C(SP-C) and variants thereof, such as SP-C(Leu), SP-C33, SP-C30 and SP-C33Leu. Other specific examples include SP-C33Leu fused to Mini-B,Mini-BLeu, 1a AA, 1b AA, 0 AAAA, 1a LL, 1b LL, 0 LLLL or SP-B proteins, optionally via a linker, e.g. Glyn, Leun, Gly-Alan or the like. SP-C33Leu may be arranged N-terminal or, preferably, C-terminal to the Mini-B,Mini-BLeu, 1a AA, 1b AA, 0 AAAA, 1a LL, 1b LL, 0 LLLL or SP-B protein Examples of protein and polypeptide drugs and drug targets according to the invention are listed in Table 7.







TABLE 7





Protein and polypeptide drugs and drug targets
















Protein
Sequence/Uniprot ID





Insulin-like growth factor IA
P01243


 


Insulin like growth factor IB
P05019


 


Growth hormone 1, variant 1
Q6IYF1


 


Growth hormone 1, variant 2
Q6IYF0


 


Growth hormone 2, variant 2
B1A4H7


 


Insulin
P01308


 


Erythropoietin
P01588


 


Coagulation Factor VIII
P00451


 


Coagulation Factor IX
P00740


 


Prothrombin
P00734


 


Serum albumin
P02768


 


Antithrombin III
P01008


 


Interferon alfa
P01563


 


Somatotropin
P01241


 


Major pollen allergen Bet v 1-A
P15494


 


OspA (Piscirickettsia salmonis)
Q5BMB7


 


17 kDa antigen variant of
Q9F9K8


OspA (P. salmonis)



 


Transforming growth factor beta-1
P01137


 


Transforming growth factor beta-2
P61812


 


Transforming growth factor beta-3
P10600


 


Interleukin 1 beta
P01584


 


Interleukin 1 alfa
P01583


 


Interleukin 2
P60568


 


Interleukin 3
P08700


 


Interleukin 4
P05112


 


Interleukin 5
P05113


 


Interleukin 6
P05231


 


Interleukin 7
P13232


 


Interleukin 8
P10145


 


Interleukin 9
P15248


 


Interleukin 10
P22301


 


Interleukin 12 subunit alfa
P29459


 


Interleukin 12 subunit beta
P29460


 


Interleukin 18
Q14116


 


Interleukin 21
Q9HBE4


 


Thymic stromal lymphopoietin
Q969D9


 


Brichos
SEQ ID NO: 41


 


Neuroserpin
SEQ ID NO: 49





Protein
Sequence





SP-C
FGIPCCPVHLKRLLIVVVVVVLIVVVIVGALLMGL a


 


SP-C(Leu)
FGIPSSPVHLKRLKLLLLLLLLILLLILGALLMGL


 


SP-C33
IPSSPVHLKRLKLLLLLLLLILLLILGALLMGL


 


SP-C30
IPSSPVHLKRLKLLLLLLLLILLLILGALL


 


SP-C33(Leu)
IPSSPVHLKRLKLLLLLLLLILLLILGALLLGL


 


LL-37
LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES


 


KL4
KLLLLKLLLLKLLLLKLLLLK


 


1a AA
CWLARALIKRIQALIPKGGRLLPQLVARLVLRCS b


 


1b AA
AWLCRALIKRIQALIPKGGRLLPQLVCRLVLRAS c


 


0 AAAA
AWLARALIKRIQALIPKGGRLLPQLVARLVLRAS


 


1a LL
CWLLRALIKRIQALIPKGGRLLPQLVLRLVLRCS b


 


1b LL
LWLCRALIKRIQALIPKGGRLLPQLVCRLVLRLS c


 


0 LLLL
LWLLRALIKRIQALIPKGGRLLPQLVLRLVLRLS





a Cys-5 and Cys-6 in native SP-C are palmitoylated


b Cys1-Cys33 linkage


c Cys4-Cys27 linkage






Examples of aggregation-prone proteins and polypeptides include avidin, streptavidin and extracellular, ligand-binding parts of cytokine receptors. Examples of aggregation-prone proteins and polypeptides according to the invention are listed in Table 8.







TABLE 8







Aggregation-prone proteins and polypeptides









Uniprot ID/


Protein
other reference





Streptavidin, Streptomyces avidinii
P22629


Streptavidin, Streptomyces lavendulae
B8YQ01


Streptavidin V1, Streptomyces venezuelae
Q53532


Streptavidin V2, Streptomyces venezuelae
Q53533


Putative Streptavidin, Burkholderia mallei
A1V7ZO


(strain SAVP1)


Putative Streptavidin,
Q2T1V4


Burkholderia thailandensis


Putative Streptavidin, Burkholderia mallei
Q62EP2


Core Streptavidin
GenBank: CAA77107.1


M4 (quadruple mutein of Streptavidin)
J Biol Chem 280(24):



23225-23231 (2005)


Avidin, Gallus gallus
P02701



GenBank: CAC34569.1


Actin
P68133


Interleukin 6 receptor subunit alfa
P08887


Interleukin 6 receptor subunit beta
P40189


Interleukin 2 receptor subunit alfa
P01589


Interleukin 2 receptor subunit beta
P14784


Cytokine receptor common subunit gamma
P31785


Green Fluorescent Protein (GFP)
SEQ ID NO: 44









Examples of proteases include protease 3C from coxsackie virus or human rhinovirus. Further examples of proteases according to the invention are listed in Table 9.







TABLE 9







Proteases











Accession


Protease
Class
no.





Trypsin (bovine)
serine
P00760


Chymotrypsin (bovine)
serine
P00766


Elastase (porcine)
serine
P00772


Endoproteinase Arg-C
serine


(mouse submaxillary gland)


Endoproteinase Glu-C (V8 protease)
serine
P04188


(Staphylococcus aureus)


Acylamino-acid-releasing enzyme (porcine)
serine
P19205


Carboxypeptidase (Penicillium janthinellum)
serine
P43946


Proteinase K (Tritirachium album)
serine
P06873


Subtilisin (Bacillus subtilis)
serine
P04189




P29122


Carboxypeptidase Y (yeast)
serine
P00729


Endoproteinase Lys-C
serine
S77957


(Lysobacter enzymogenes)


Enteropeptidase (human)
serine
P98073


Prothrombin
serine
P00734


Factor X
serine
P00742


Pepsin
aspartic
P00791




P00790


Cathepsin D (human)
aspartic
P07339


HIV-1 protease
aspartic
Q9YQ34


Cathepsin C
cysteine


Clostripain (endoproteinase-Arg-C)
cysteine
P09870


(Clostridium histolyticum)


Papain (Carica papaya)
cysteine
P00784


Protease 3C
cysteine
Q04107


Tobacco Etch virus (TEV)
cysteine
Q0GDU8


Thermolysin (Bacillus thermo-proteolyticus)
metallo
P00800


Endoproteinase Asp-N (Pseudomonas fragi)
metallo
Q9R4J4


Carboxypeptidase A (bovine)
metallo
P00730


Carboxypeptidase B (porcine)
metallo
P00732


IgA protease
metallo
Q97QP7









In preferred embodiments of the invention, the desired non-spidroin protein is selected from surfactant protein B (SP-B) and variants thereof, such as Mini-B, Mini-B27, Mini-BLeu, KL4, LL-37, and surfactant protein C(SP-C) and variants thereof, such as SP-C(Leu), SP-C33, SP-C30 and SP-C33Leu. Other preferred non-spidroin proteins according to the invention are neuroserpin, GFP, and the 1a AA, 1b AA, 0 AAAA, 1a LL, 1b LL and 0 LLLL proteins.
In certain preferred embodiments of the invention, the fusion protein is selected from the group consisting of SEQ ID NOS 26, 28, 30, 34, 37, 39, 42 and 47; and proteins having at least 80%, preferably at least 90%, more preferably at least 95% identity, to any of these proteins.
According to another aspect, the present invention provides an isolated polynucleic acid encoding a fusion protein according to the invention. In a preferred embodiment, the isolated polynucleic acid is selected from the group consisting of SEQ ID NOS 27, 29, 31, 38, 40, 43 and 48. In another preferred embodiment, the isolated polynucleic acid is selected from the group consisting of SEQ ID NOS 14-16, 18 and 24.
According to one aspect, the present invention provides a novel use of at least one moiety which is derived from the N-terminal (NT) fragment of a spider silk protein as a solubility enhancing moiety in a fusion protein for production of a desired protein or polypeptide. In a preferred embodiment, the desired protein or polypeptide is a spidroin protein or polypeptide. When the fusion protein comprises a single solubility-enhancing moiety which is derived from the N-terminal (NT) fragment of a spider silk protein, then it is a preferred alternative that the desired protein is a non-spidroin protein or polypeptide. In one preferred embodiment, the desired protein or polypeptide is a non-spidroin protein or polypeptide.
According to another aspect, the present invention provides a method of producing a fusion protein. The first step involves expressing in a suitable host a fusion protein according to the invention. Suitable hosts are well known to a person skilled in the art and include e.g. bacteria and eukaryotic cells, such as yeast, insect cell lines and mammalian cell lines. Typically, this step involves expression of a polynucleic acid molecule which encodes the fusion protein in E. coli. 
The second method step involves obtaining a mixture containing the fusion protein. The mixture may for instance be obtained by lysing or mechanically disrupting the host cells. The mixture may also be obtained by collecting the cell culture medium, if the fusion protein is secreted by the host cell. The thus obtained protein can be isolated using standard procedures. If desired, this mixture can be subjected to centrifugation, and the appropriate fraction (precipitate or supernatant) be collected. The mixture containing the fusion protein can also be subjected to gel filtration, chromatography, e.g. anion exchange chromatography, dialysis, phase separation or filtration to cause separation. Optionally, lipopolysaccharides and other pyrogens are actively removed at this stage. If desired, linker peptides may be removed by cleavage in this step.
In a preferred embodiment, the obtained mixture comprises the fusion protein dissolved in a liquid medium, typically a salt buffer or cell culture medium. In one preferred embodiment, the mixture has a pH below 6.3, and preferably below 6, which promotes assembly of soluble NT domains. In another preferred embodiment, the mixture has a pH above 6.4, and preferably above 7, which prevents or decreases assembly of soluble NT domains. A pH above 6.4, such as above 7, may be particularly useful to improve solubility of fusion proteins according to the invention wherein the desired protein/polypeptide is derived from a spidroin protein or wherein the desired protein/polypeptide is an amyloid-forming or aggregation-prone protein/polypeptide.
According to a related aspect, the present invention provides a method of producing a desired protein or polypeptide. The first step involves expressing in a suitable host a fusion protein according to the invention. Suitable hosts are well known to a person skilled in the art and include e.g. bacteria and eukaryotic cells, such as yeast, insect cell lines and mammalian cell lines. Typically, this step involves expression of a polynucleic acid molecule which encodes the fusion protein in E. coli. 
The second method step involves obtaining a mixture containing the fusion protein. The mixture may for instance be obtained by lysing or mechanically disrupting, e.g. sonicating, the host cells. The mixture may also be obtained by collecting the cell culture medium, if the fusion protein is secreted by the host cell. The thus obtained protein can be isolated using standard procedures. If desired, this mixture can be subjected to centrifugation, and the appropriate fraction (precipitate or supernatant) be collected. The mixture containing the fusion protein can also be subjected to gel filtration, chromatography, e.g. anion exchange chromatography, dialysis, phase separation or filtration to cause separation. Optionally, lipopolysaccharides and other pyrogens are actively removed at this stage. If desired, linker peptides may be removed by cleavage in this step. As set out above, this may be the most suitable form of the desired protein or polypeptide, i.e. as part of a fusion protein. It may provide a suitable handle for purification and detection and/or provide desirable properties, e.g. stability and in particular solubility.
In a preferred embodiment, the method may also comprise the step of cleaving the fusion protein to provide the desired protein or polypeptide. In this embodiment, the fusion protein is comprising at least one cleavage site arranged between at least one desired protein or polypeptide moiety and at least one solubility-enhancing moiety. In a typical fusion protein, this implies the presence of a single cleavage site between the solubility-enhancing moiety or moieties and the desired protein or polypeptide. Cleavage may be achieved using standard procedures, for instance cleavage by cyanogen bromide (CNBr) after Met residues, cleavage by hydroxylamine between Asn and Gly residues, cleavage by protease 3C between Gln and Gly residues at—XLETLFQGX—(SEQ ID NO: 120) sites, and at various other protease sites that are well known to the person skilled in the art.
The thus obtained desired protein or polypeptide can be isolated using standard procedures. If desired, this mixture can be subjected to centrifugation, and the appropriate fraction (precipitate or supernatant) be collected. The mixture containing the desired protein or polypeptide can also be subjected to gel filtration, chromatography, dialysis, phase separation or filtration to cause separation. Optionally, lipopolysaccharides and other pyrogens are actively removed at this stage. If desired, linker peptides may be removed by cleavage in this step.
In a preferred embodiment, the obtained mixture comprises the fusion protein dissolved in a liquid medium, typically a salt buffer or cell culture medium. In one preferred embodiment, the mixture has a pH below 6.3, and preferably below 6, such as in the interval 4.2-6.3 or 4.2-6, which promotes assembly of soluble NT domains. In another preferred embodiment, the mixture has a pH above 6.4, and preferably above 7, which prevents or decreases assembly of soluble NT domains. A pH above 6.4, such as above 7, may be particularly useful to improve solubility of fusion proteins according to the invention wherein the desired protein/polypeptide is derived from a spidroin protein or wherein the desired protein/polypeptide is an amyloid-forming or aggregation-prone protein/polypeptide.
Thus, the fusion protein is typically obtained as a solution in a liquid medium. By the terms “soluble” and “in solution” is meant that the fusion protein is not visibly aggregated and does not precipitate from the solvent at 60 000×g. The liquid medium can be any suitable medium, such as an aqueous medium, preferably a physiological medium, typically a buffered aqueous medium, such as a 10-50 mM Tris-HCl buffer or phosphate buffer. The liquid medium preferably has a pH of 6.4 or higher, such as 7 or higher, and/or an ion composition that prevents polymerisation of the solubility-enhancing moiety. That is, the liquid medium typically has either a pH of 6.4 or higher, such as 7 or higher, or an ion composition that prevents polymerisation of the solubility-enhancing moiety, or both.
Ion compositions that prevent polymerisation of the solubility-enhancing moiety can readily be prepared by the skilled person. A preferred ion composition that prevents polymerisation of the solubility-enhancing moiety has an ionic strength of more than 300 mM. Specific examples of ion compositions that prevent polymerisation of the solubility-enhancing moiety include above 300 mM NaCl, 100 mM phosphate and combinations of these ions having desired preventive effect on the polymerisation of the solubility-enhancing moiety, e.g. a combination of 10 mM phosphate and 300 mM NaCl.
It has been surprisingly been found that the presence of an solubility-enhancing moiety improves the stability of the solution and prevents polymer formation under these conditions. This can be advantageous when immediate polymerisation may be undesirable, e.g. during protein purification, in preparation of large batches, or when other conditions need to be optimized. It is preferred that the pH of the liquid medium is adjusted to 6.7 or higher, such as 7.0 or higher to achieve high solubility of the fusion protein. It can also be advantageous that the pH of the liquid medium is adjusted to the range of 6.4-6.8, which provides sufficient solubility of the spider silk protein but facilitates subsequent pH adjustment to 6.3 or lower.
Another aspect of the invention is based on the insight that the NT domain will form large soluble assemblies when the pH is lowered from ca 7 to 6, or more specifically from above 6.4 to below 6.3. This assembly occurs most efficiently at a pH above 4.2, i.e. in the range of 4.2-6.3, such as 4.2-6. This property can be used for affinity purification, e.g. if NT is immobilized on a column. This approach allows release of bound proteins by a shift in pH within a physiologically relevant interval, since the assembly will resolve when pH is elevated from ca 6 to 7.
In a preferred embodiment of the methods according to the invention, the step of isolating the fusion protein involves purification of the fusion protein on an affinity medium, such as an affinity column, with an immobilized NT moiety and/or on an anion exchange medium, such as an anion exchange column. Purification of the fusion protein on an affinity medium is preferably carried out with association to an affinity medium with an immobilized NT moiety at a pH of 6.3 or lower, preferably in the range of 4.2-6.3, followed by dissociation from the affinity medium with a desired dissociation medium, e.g. having a pH of 6.4 or higher, a pH of 4.1 or lower and/or having a high ionic strength. Purification of the fusion protein on an anion exchange medium is preferably carried out with association to the anion exchange medium at a pH of 6.4 or higher, followed by dissociation from the anion exchange medium with a dissociation medium having a high ionic strength. If desired, purification of the fusion protein on an affinity medium, such as an affinity column, with an immobilized NT moiety can be combined with purification on an anion exchange medium, such as an anion exchange column. A dissociation medium having high ionic strength typically has an ionic strength of more than 300 mM, such as above 300 mM NaCl.
These two affinity-based procedures utilize the inherent properties of the solubility-enhancing moiety according to the invention. Of particular interest is the strong tendency of spidroin NT protein fragments to associate at a pH below 6.3, in particular in the range of 4.2-6.3. This can advantageously be utilized as a powerful affinity purification tool, allowing one-step purification of fusion proteins according to the invention from complex mixtures. Although chromatography is preferred, other affinity-based purification methods than chromatography can obviously be employed, such as magnetic beads with functionalized surfaces or filters with functionalized surfaces.
This insight that the NT domain will form large soluble assemblies when the pH is lowered from ca 7 to 6, or more specifically from above 6.4 to below 6.3, preferably in the range of 4.2-6.3, such as 4.2-6, is also useful when it is desired to promote assembly of NT-containing proteins, such as in a method of producing macroscopic polymers, e.g. fibers, films, foams, nets or meshes, of a spider silk protein such as those disclosed herein. A preferred method of producing polymers of an isolated spider silk protein, is comprising the steps of:

    (i) providing a spider silk protein consisting of from 170 to 600 amino acid residues and comprising:
    
        an N-terminal fragment of from 100 to 160 amino acid residues derived from the N-terminal fragment of a spider silk protein; and
        a repetitive fragment of from 70 to 300 amino acid residues derived from the repetitive fragment of apidroin protein; and optionally
        a C-terminal fragment of from 70 to 120 amino acid residues, which fragment is derived from the C-terminal fragment of a spider silk protein;
    
    
    (ii) providing a solution of said spider silk protein in a liquid medium at pH 6.4 or higher and/or an ion composition that prevents polymerisation of said spider silk protein, optionally involving removal of lipopolysaccharides and other pyrogens;
    (iii) adjusting the properties of said liquid medium to a pH of 6.3 or lower, such as 4.2-6.3, and an ion composition that allows polymerisation of said spider silk protein;
    (iv) allowing the spider silk protein to form solid polymers in the liquid medium, said liquid medium having a pH of 6.3 or lower, such as 4.2-6.3, and an ion composition that allows polymerisation of said spider silk protein; and
    (v) isolating the solid spider silk protein polymers from said liquid medium.


The present invention will in the following be further illustrated by the following non-limiting examples.
EXAMPLES
Example 1
Production of an SP-C33Leu Fusion Protein
An expression vector was constructed comprising a gene encoding NT-MetSP-C33Leu as a fusion to His6 (SEQ ID NOS: 26-27). The vector was used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that were grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of 0.9-1, induced with isopropyl-β-D-thiogalactopyranoside (IPTG), and further incubated for 3 hours at 25° C. The cells were harvested by centrifugation and resuspended in 20 mM Tris-HCl, pH 8.
Lysozyme was added, and the cells were incubated for 30 min on ice. Tween was added to a final concentration of 0.7%. The cells were disrupted by sonication on ice for 5 min, alternating 2 seconds on and 2 seconds off. The cell lysate was centrifuged at 20 000×g for 30 min. The supernatant was loaded on a Ni-NTA sepharose column, equilibrated with 20 mM Tris-HCl, pH 8 buffer containing 0.7% Tween. The column was washed with 20 mM Tris-HCl, pH 8 buffer containing 0.7% Tween, and the bound protein was eluted with 20 mM Tris-HCl pH 8, 300 mM imidazole buffer containing 0.7% Tween.
The eluate was subjected to SDS-PAGE on a 12% Tris-Glycine gel under reducing conditions. A major band corresponding to the fusion protein is indicated by the arrow in FIG. 3A. The yield was determined by mg purified protein from 1 liter shake flask culture grown to an OD600 of 1. The yield was 64 mg/l. It is concluded that a fusion protein containing a single NT moiety results in surprisingly high yield in the presence of detergent in the cell lysate.
Example 2
Production of an SP-C33Leu Fusion Protein
An expression vector was constructed comprising a gene encoding NT2-MetSP-C33Leu (i.e. NTNT-MetSP-C33Leu) as a fusion to His6 (SEQ ID NOS: 28-29). The vector was used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that were grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of 0.9-1, induced with isopropyl-β-D-thiogalactopyranoside (IPTG), and further incubated for 3 hours at 25° C. The cells were harvested by centrifugation and resuspended in 20 mM Tris-HCl, pH 8.
Lysozyme was added, and the cells were incubated for 30 min on ice.
Tween was either not added or added to a final concentration of 0.7%. The cells were disrupted by sonication on ice for 5 min, alternating 2 seconds on and 2 seconds off. The cell lysate was centrifuged at 20 000×g for 30 min. The supernatants were loaded on a Ni-NTA sepharose column, equilibrated with 20 mM Tris-HCl, pH 8 buffer±0.7% Tween. The column was washed with 20 mM Tris-HCl, pH 8 buffer±0.7% Tween, and the bound protein was eluted with 20 mM Tris-HCl pH 8, 300 mM imidazole buffer±0.7% Tween.
The eluate was subjected to SDS-PAGE on a 12% Tris-Glycine gel under reducing conditions. A major band corresponding to the fusion protein is indicated by the arrow in FIG. 3B. The yield was determined by mg purified protein from 1 liter shake flask culture grown to an OD600 of 1. The yield was 40 mg/l in the absence of Tween, and 68 mg/l in the presence of 0.7% Tween. It is concluded that a fusion protein containing two consecutive NT moieties results in surprisingly high yield in the absence of detergent in the cell lysate, and an even further increased yield in the presence of detergent in the cell lysate.
Example 3
Production of SP-C33Leu Fusion Proteins
Expression vectors are constructed comprising a gene encoding NT-MetSP-C33Leu, NT2-MetSP-C33Leu and NT-MetSP-C33Leu-NT, respectively. The vectors are used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that are grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of 0.9-1, induced with isopropyl-β-D-thiogalactopyranoside (IPTG), and further incubated for 3 hours at 25° C. The cells are harvested by centrifugation and resuspended in 20 mM Tris-HCl, pH 8.
Lysozyme is added, and the cells are incubated for 30 min on ice. Tween is either not added or added to a final concentration of 0.7%. The cells are disrupted by sonication on ice for 5 min, alternating 2 seconds on and 2 seconds off. The cell lysates are centrifuged at 20 000×g for 30 min.
Example 4
Preparation of NT-Sepharose
A CysHis6NT construct is used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences). The cells are grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of 0.8-1, induced with isopropyl-β-D-thiogalactopyranoside (IPTG), and further incubated for up to 4 hours at room temperature. Thereafter, cells are harvested and resuspended in 20 mM Tris-HCl, pH 8.0, supplemented with lysozyme and DNase I. After complete lysis, the 15000 g supernatants are loaded on a column packed with Ni sepharose (GE Healthcare). The column is washed extensively, and then bound proteins are eluted with 100-300 mM imidazole. Fractions containing the target proteins are pooled and dialyzed against 20 mM Tris-HCl, pH 8.0. Purified Cys-His6-NT protein is coupled to activated thiol Sepharose using standard protocol (GE Healthcare).
Example 5
Purification of Fusion Proteins Using Nt Sepharose
Cell lysates from Example 3 are loaded on a column packed with NT sepharose, pre-equilibrated with 20 mM NaPi, pH 6. The column is washed extensively with 20 mM NaPi, pH 6 and then bound proteins are eluted with 20 mM NaPi, pH 7. Fractions containing the target proteins are pooled. Protein samples are separated on SDS-PAGE gels and then stained with Coomassie Brilliant Blue R-250. Protein content is determined from absorbance at 280 nm.
Example 6
Purification of Fusion Proteins on Anion Exchanger
Cell lysates from Example 3 are loaded on a HiTrap Q FF column (GE Healthcare), pre-equilibrated with 20 mM NaP pH 6.5. The column is washed extensively and then bound proteins are eluted with a linear gradient of NaCl up to 1 M. Fractions containing the target proteins are pooled. Protein samples are separated on SDS-PAGE gels and then stained with Coomassie Brilliant Blue R-250. Protein content is determined from absorbance at 280 nm.
Example 7
Cleavage and Isolation of Desired Protein
The fusion proteins of Examples 3, 5 and 6 are dissolved in 70% aqueous formic acid, supplemented with 0.1 g/ml CNBr and left at room temp. for 24 hours. Thereafter the mixtures are dried, and separated in the two-phase system chloroform/methanol/water, 8:4:3, by vol. SP-C33Leu is found in the organic phase and can thereafter optionally be further purified with reversed-phase HPLC using a C18 column. The activity of SP-C33Leu mixed with synthetic phospholipids can be tested in vitro or in vivo, as described in e.g. J. Johansson et al., J. Appl. Physiol. 95, 2055-2063 (2003).
Example 8
Production of LL-37 Fusion Protein
An expression vector was constructed comprising a gene encoding NT2-LL37 (i.e. NTNT-LL37) as a fusion to His6 (SEQ ID NOS: 30-31). The vector was used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that were grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of 0.9-1, induced with isopropyl-β-D-thiogalactopyranoside (IPTG), and further incubated for 3 hours at 25° C. The cells were harvested by centrifugation and resuspended in 20 mM Tris-HCl, pH 8.
Lysozyme was added, and the cells were incubated for 30 min on ice. The cells were disrupted by sonication on ice for 5 min, alternating 2 seconds on and 2 seconds off. The cell lysate was centrifuged at 20 000×g for 30 min. The supernatants were loaded on a Ni-NTA sepharose column, equilibrated with 20 mM Tris-HCl, pH 8, 250 mM NaCl buffer. The column was washed with 20 mM Tris-HCl, pH 8, 250 mM NaCl buffer, and the bound protein was eluted with 20 mM Tris-HCl pH 8, 300 mM imidazole buffer.
Example 9
Production of NT-REP4-CT
An expression vector was constructed to produce NT-REP4-CT as an N-terminal fusion to His6 (SEQ ID NOS 17-18). The vector was used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that were grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of  ̃1, induced with isopropyl-β-D-thiogalactopyranoside (IPTG), and further incubated for up to 4 hours at room temperature. Thereafter, cells were harvested and resuspended in 20 mM Tris-HCl (pH 8.0) supplemented with lysozyme and DNase I.
After complete lysis, the 15000 g supernatants were loaded onto a column packed with Ni-Sepharose (GE Healthcare, Uppsala, Sweden). The column was washed extensively before bound proteins were eluted with 300 mM imidazole. Fractions containing the target proteins were pooled and dialyzed against 20 mM Tris-HCl (pH 8.0).
Protein samples were separated via SDS-PAGE and then stained with Coomassie Brilliant Blue R-250. The resulting NT-REP4-CT protein was concentrated by ultrafiltration using a 5 kDa molecular mass cutoff cellulose filter (Millipore).
Example 10
Production of NT-REP4-CT
An expression vector was constructed to produce NT-REP4-CT as a C-terminal fusion to Zbasic (SEQ ID NO 19). The vector was used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that were grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of  ̃1, induced with isopropyl-β-D-thiogalactopyranoside (IPTG), and further incubated for up to 2-4 hours at room temperature. Thereafter, cells were harvested and resuspended in 50 mM Na phosphate (pH 7.5) supplemented with lysozyme and DNase I.
After complete lysis, the 15000 g supernatants were loaded onto cation exchanger (HiTrap S, GE Healthcare, Uppsala, Sweden). The column was washed extensively before bound proteins were eluted with a gradient against 500 mM NaCl. Fractions containing the target proteins were pooled and dialyzed against 50 mM Na phosphate (pH 7.5). The NT-REP4-CT protein (SEQ ID NO 20) was released from the Zbasic tags by proteolytic cleavage using a protease 3C:fusion protein ratio of 1:50 (w/w) at 4° C. over night. To remove the released Zbasic tag, the cleavage mixture was loaded onto a second cation exchanger, and the flowthrough was collected.
Example 11
Production of NT-REP4-CT
An expression vector was constructed to produce NT-REP4-CT as an
C-terminal fusion to H isTrxHis (SEQ ID NO 21). The vector was used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that were grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of  ̃1, induced with isopropyl-β-D-thiogalactopyranoside (IPTG), and further incubated for up to 2-4 hours at room temperature. Thereafter, cells were harvested and resuspended in 20 mM Tris-HCl (pH 8.0) supplemented with lysozyme and DNase I.
After complete lysis, the 15000 g supernatants were loaded onto column packed with Ni-Sepharose (GE Healthcare, Uppsala, Sweden). The column was washed extensively before bound proteins were eluted with a gradient against 500 mM NaCl. Fractions containing the target proteins were pooled and dialyzed against 20 mM Tris-HCl (pH 8.0). The NT-REP4-CT protein (SEQ ID NO 22) was released from the HisTrxHis tags by proteolytic cleavage using a thrombin:fusion protein ratio of 1:1000 (w/w) at 4° C. over night. To remove the released H isTrxHis, the cleavage mixture was loaded onto a second Ni-Sepharose column, and the flowthrough was collected.
Example 12
Production of NT2-REP4-CT
An expression vector was constructed comprising a gene encoding NT2-REP4-CT (i.e. NTNT-REP4-CT) as a fusion to His6 (SEQ ID NOS: 23-24). The vector was used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that were grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of 0.9-1, induced with isopropyl-β-D-thiogalactopyranoside (IPTG), and further incubated for 3 hours at 25° C. The cells were harvested by centrifugation and resuspended in 20 mM Tris-HCl, pH 8.
Lysozyme and DNase were added, and the cells were incubated for 30 min on ice. The cell lysate was centrifuged at 20 000×g for 30 min. The supernatants were loaded on a Ni-NTA sepharose column, equilibrated with 20 mM Tris-HCl, pH 8 buffer. The column was washed with 20 mM Tris-HCl, pH 8 buffer, and the bound protein was eluted with 20 mM Tris-HCl pH 8, 300 mM imidazole buffer.
The eluate was subjected to SDS-PAGE on a 12% Tris-Glycine gel under reducing conditions. A major band corresponding to the fusion protein is indicated by the arrow in FIG. 3C. The yield was determined by mg purified protein from 1 liter shake flask culture grown to an OD600 of 1. The yield was 30 mg/l. It is concluded that spidroin miniature proteins can advantageously be expressed as fusions with two NT moieties.
Example 13
Production of NT-REP4-CT NT2-REP4-CT and NT-REP8-CT
Expression vectors are constructed comprising a gene encoding NT-REP4-CT (SEQ ID NOS 20 and 22), NT2-REP4-CT (SEQ ID NO 23), and NT-REP8-CT (SEQ ID NO: 25), respectively. The vectors are used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that are grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of 0.9-1, induced with isopropyl-β-D-thiogalactopyranoside (IPTG), and further incubated for 3 hours at 25° C. The cells are harvested by centrifugation and resuspended in 20 mM Tris-HCl, pH 8.
Lysozyme is added, and the cells are incubated for 30 min on ice. Tween is either not added or added to a final concentration of 0.7%. The cell lysates are centrifuged at 20 000×g for 30 min. One portion of the supernatant is loaded on an anion exchange column in accordance with Example 6.
An NT affinity medium is prepared as described in Example 4. Another portion of the supernatant is loaded on an NT affinity column in accordance with Example 5.
Eluates from the anion exchange column and the NT affinity column are subjected to gel electrophoresis.
Example 14
Production of NTHis NT2-REP8-CT and NT2-Brichos
A) NTHis
An expression vector was constructed to produce NT as an N-terminal fusion to His6 (SEQ ID NO 32). The vector was used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that were grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of  ̃1, induced with isopropyl-β-D-thiogalactopyranoside (IPTG), and further incubated for up to 4 hours at room temperature. Thereafter, cells were harvested and resuspended in 20 mM Tris-HCl (pH 8.0) supplemented with lysozyme and DNase I.
After complete lysis, the 15000 g supernatants were loaded onto a column packed with Ni-Sepharose (GE Healthcare, Uppsala, Sweden). The column was washed extensively before bound proteins were eluted with 300 mM imidazole. Fractions containing the target proteins were pooled and dialyzed against 20 mM Tris-HCl (pH 8.0). Protein samples were separated via SDS-PAGE and then stained with Coomassie Brilliant Blue R-250. The resulting NT protein (SEQ ID NO 32) was concentrated by ultrafiltration using a 5 kDa molecular mass cutoff cellulose filter (Millipore). The yield was 112 mg/liter shake flask grown to an OD600 of 1.
B) NT2-REP8-CT
An expression vector was constructed to produce NT2-REP8-CT (NTNT8REPCT) as an N-terminal fusion to His6 (SEQ ID NO 33). The vector were used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that were grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of  ̃1, induced with isopropyl-β-D-thiogalactopyranoside (IPTG), and further incubated for up to 4 hours at room temperature. Thereafter, cells were harvested and resuspended in 20 mM Tris-HCl (pH 8.0) supplemented with lysozyme and DNase I. Protein samples were separated via SDS-PAGE and then stained with Coomassie Brilliant Blue R-250 to confirm protein expression.
After complete lysis, the 15000 g supernatants are loaded onto a column packed with Ni-Sepharose (GE Healthcare, Uppsala, Sweden). The column is washed extensively before bound proteins are eluted with 300 mM imidazole. Fractions containing the target proteins are pooled and dialyzed against 20 mM Tris-HCl (pH 8.0). Protein samples are separated via SDS-PAGE and then stained with Coomassie Brilliant Blue R-250.
C) NT2-Brichos
An expression vector was constructed to produce NT2-Brichos (NT-NT-Brichos) as an N-terminal fusion to His6 (SEQ ID NO 34). The vector was used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that were grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of  ̃1, induced with isopropyl-β-D-thiogalactopyranoside (IPTG), and further incubated for up to 4 hours at room temperature. Thereafter, cells were harvested and resuspended in 20 mM Tris-HCl (pH 8.0) supplemented with lysozyme and DNase I. The cells were further disrupted by sonication on ice for 5 minutes, 2 seconds on and 2 seconds off.
After complete lysis, the 15000 g supernatants were loaded onto a column packed with Ni-Sepharose (GE Healthcare, Uppsala, Sweden). The column was washed extensively before bound proteins were eluted with 300 mM imidazole. Fractions containing the target proteins were pooled and dialyzed against 20 mM Tris-HCl (pH 8.0). Protein samples were separated via SDS-PAGE and then stained with Coomassie Brilliant Blue R-250. The resulting NT2-Brichos protein (SEQ ID NO 34) was concentrated by ultrafiltration using a 5 kDa molecular mass cutoff cellulose filter (Millipore). The yield was 20 mg/liter shake flask grown to an OD600 of 1.
Example 15
NT for pH-Dependent, Reversible Capture
Purpose: Use covalently immobilised NT (and NTNT) to reversibly capture NT fusion proteins.
Strategy: Investigate pH dependent assembly of NT (and NTNT) fusion proteins to fibers (and film) with covalently linked NT (and NTNT). Fibers and films without NT are used as control.
A) Fibers
Fibers ( ̃0.5 cm long,  ̃50 μg) of NT-REP4-CT (SEQ ID NO 20), NT2-REP4-CT (SEQ ID NO 23) and REPO-CT (SEQ ID NO 2, control) were submerged in 100 μl solution of 5 mg/ml soluble NTHis (SEQ ID NO 32) or NT2-Brichos (SEQ ID NO 34) at pH 8 for 10 minutes. The pH was decreased by addition of 400 μl sodium phosphate buffer (NaP) to pH 6 and incubated for 10 minutes to allow assembly of soluble NT to the fiber. The fibers were transferred to 500 μl of NaP at pH 6, and washed twice. Finally, the fibers were transferred to 500 μl of NaP at pH 7, and incubated 10 minutes to allow release of soluble NT. The same was done in the presence of 300 mM NaCl in all pH 6 NaP buffers. Samples from the different solutions were analysed on SDS-PAGE.
Using the NT2-REP4-CT and NT-REP4-CT fibers, both NTHis and NT2-Brichos were captured at pH 6. Upon pH raise to pH 7, both NTHis and NT2-Brichos) were released again and could be detected on SDS-PAGE. The addition of 300 mM NaCl decreased capture at pH 6.
B) Film:
Films of NT-REP4-CT (SEQ ID NO 20) and REPO-CT (SEQ ID NO 2, control) were prepared by casting 50 μl of a protein solution of 3 mg/ml in a plastic well and left to dry over night. The next day, 100 μl solution of 5 mg/ml soluble NTHis (SEQ ID NO 32) at pH 8 was added to wells with film, and left for 10 minutes. The pH was then decreased to 6 by addition of 400 μl NaP and incubated for 10 minutes to allow assembly of soluble NT to the film. The films were then washed twice with 500 μl of NaP at pH 6. For release of soluble NTHis, 500 μl of NaP at pH 7 was added and incubated for 10 minutes. The same was done in presence of 300 mM NaCl in all pH 6 NaP buffers. Samples from the different solutions were analysed on SDS-PAGE.
Analysis on SDS-PAGE showed that a NT-REP4-CT film allowed NTHis to be captured at pH 6 and released again upon raise of the pH to 7.
Example 16
NT for pH-dependent, Reversible Assembly of Fusion Proteins
Purpose: Use NT as a reversible tag that allows analysis of interaction between protein moieties, e.g. analyse the interaction of Brichos with targets with beta sheet structures e.g. surfactant protein C(SP-C).
NT2-Brichos (SEQ ID NO 34) is mixed with either NT2-MetSP-C33Leu (SEQ ID NO 28) or NTHis (SEQ ID NO 32) to a total volume of 100 μl at pH 8. NaP buffer (400 μl) is added to give a final pH of 6, and the mixture is incubated for 20 minutes to allow NT assembly. The pH is then raised again to pH 7 to allow reversal of NT assembly. Samples from the different solutions are analysed on native gel and size exclusion chromatography (SEC).
Example 17
Cleavage of NT-MetSP-C33Leu and Isolation of SP-C33Leu
About 58 mg of lyophilized HisNT-MetSP-C33Leu (SEQ ID NOS: 26) obtained in Example 1 was dissolved in 3 ml of 70% aqueous formic acid by vortexing and sonication. To this solution, 200 μl of 5 M CNBr in acetonitrile was added, and the mixture was incubated at room temperature for 24 h. Thereafter solvents were evaporated under a stream of nitrogen, and the residue was washed three times by solubilisation in 70% aqueous formic acid and drying under nitrogen.
To the dried residue was then added 4.56 ml of chloroform/methanol/water (8:4:3, by vol), after which the mixture was vortexed and centrifuged. The upper phase was removed, and 1 ml of chloroform/methanol/water (8:4:3, by vol) was added to the lower phase, and vortexing, centrifugation and removal of upper phase were repeated. The two upper phases were combined and dried under vacuum. The lower phase was dried under nitrogen.
The contents of the lower (left lane) and upper (right lane) phases were analyzed by SDS-PAGE (FIG. 4). This showed that the lower phase contains one major band with an estimated molecular mass that agrees well with that of SP-C33Leu. The identity of SP-C33Leu was confirmed by ESI mass spectrometry and amino acid sequencing, which showed a monoisotopic mass of 3594.6 Da (calculated 3594.4 Da) and the expected amino acid sequence.
Example 18
Analysis of Surface Activity of Sp-C33Leu/Phospholipid Mixture
1,2-Dipalmitoyl-sn-glycero-3-phosphocholine (DPPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) (68:31, w/w) was dissolved in chloroform:methanol (1:1, v/v) and mixed with SP-C33Leu (obtained in Example 17) in the same solvent. The peptide content in the preparations was 2% in relation to the phospholipid weight. The solvents were evaporated with nitrogen, and the preparations were resuspended in saline to a final phospholipid concentration of 10 mg/ml by slow rotation at 37° C.
Surface tension was measured in triplicates in an alveolus by a captive bubble surfactometer (CBS) (Schurch S et al., J. Appl. Physiol. 67: 2389-2396, 1989). In the CBS, surfactant and an air-bubble representing the lung alveolus are present in an air-tight enclosed chamber. To evaluate surface activity under dynamic circumstances, the chamber is compressed and surface tension can be calculated by studying the shape and height/width ratio of the bubble.
In the experiment, 2 μl of the SP-C33Leu surfactant preparation (10 mg/ml) was inserted into the sucrose-filled test chamber. After insertion, an air-bubble was created and surface tension was measured during five minutes of adsorption. In the following quasi-static cycling experiments, the bubble was compressed stepwise from the initial volume until a surface tension less than 5 mN/m was reached, alternatively to a maximum area compression of 50% and then expanded during five cycles.
The results are illustrated in FIG. 5, where the first and fifth cycle from one representative example out of three measurements are shown. The surface activity of the SP-C33Leu/DPPC/POPG mixture (FIG. 5) was very similar to that of synthetic SP-C33 in the same phospholipid mixture, see e.g. Johansson et al, J. Appl. Physiol, 95: 2055-2063 (2003).
Example 19
Production of an SP-C33Leu Fusion Protein
A) Without NT (Comparative Example)
An expression vector was constructed comprising a gene encoding Thioredoxin (TRX)-SP-C33Leu as a fusion to 2×His6 (SEQ ID NOS: 35-36). The vector was used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that were grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of 0.9-1, induced with IPTG and further incubated for 3 hours at 25° C. The cells were harvested and resuspended in 20 mM Tris-HCl (pH 8.0).
Lysozyme was added, and the cells were incubated for 30 min on ice. Tween was added to a final concentration of 0.7%. The cells were disrupted by sonication on ice for 5 min, alternating 2 sec on and 2 sec off. The cell lysate was centrifuged at 20 000×g for 30 min. The supernatants were loaded onto a column packed with Ni-Sepharose (GE Healthcare, Uppsala, Sweden), equilibrated with 20 mM Tris-HCl (pH 8.0)+0.7% Tween. The column was washed extensively before bound proteins were eluted with a 300 mM imidazole+0.7% Tween.
The target protein was eluted with 300 mM imidazole+0.7% Tween and analyzed by SDS-PAGE (FIG. 6A). The eluate contained a small and impure amount of target protein.
B) With NT
An expression vector was constructed comprising a gene encoding TRX-NT-SP-C33Leu as a fusion to 2×His6 (SEQ ID NOS:37-38). The vector was used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that were grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of 0.9-1, induced with IPTG, and further incubated for 3 hours at 25° C. The cells were harvested and resuspended in 20 mM Tris-HCl (pH 8.0).
Lysozyme was added, and the cells were incubated for 30 min on ice. Tween was added to a final concentration of 0.7%. The cells were disrupted by sonication on ice for 5 min, alternating 2 sec on and 2 sec off. The cell lysate was centrifuged at 20 000×g for 30 min. The supernatants were loaded onto a column packed with Ni-Sepharose (GE Healthcare, Uppsala, Sweden), equilibrated with 20 mM Tris-HCl (pH 8.0)+0.7% Tween. The column was washed extensively before bound proteins were eluted with a 300 mM imidazole+0.7% Tween. Fractions containing the fusion proteins were pooled and dialyzed against deionized water.
The eluate was subjected to SDS-PAGE on a 12% Tris-Glycine gel under reducing conditions. A major band corresponding to the protein is indicated by the arrow in FIG. 6B. The yield was determined by mg purified protein from 1 liter shake flask culture grown to an OD600 of 1. The yield was 30 mg/l.
Example 20
Production of Brichos
An expression vector was constructed comprising a gene encoding NT2-Brichos (i.e. NTNT-Brichos) as a fusion to His6LinkHis6 (SEQ ID NOS:39-40). The vector was used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that were grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of 0.9-1, induced with IPTG, and further incubated for 3 hours at 25° C. The cells were harvested and resuspended in 20 mM Tris-HCl (pH 8.0).
Lysozyme was added, and the cells were incubated for 30 min on ice. The cells were disrupted by sonication on ice for 5 min, alternating 2 sec on and 2 sec off. The cell lysate was centrifuged at 20 000×g for 30 min. The supernatants were loaded onto a column packed with Ni-Sepharose (GE Healthcare, Uppsala, Sweden). The column was washed extensively before bound proteins were eluted with a 300 mM imidazole. Fractions containing the fusion proteins were pooled and dialyzed against 20 mM Tris-HCl (pH 8.0).
The eluate was subjected to SDS-PAGE on a 12% Tris-Glycine gel under reducing conditions. A major band corresponding to the fusion protein is indicated by the arrow in FIG. 7. The yield was determined by mg purified protein from 1 liter shake flask culture grown to an OD600 of 1. The yield was 28 mg/l of the fusion protein.
The Brichos protein (SEQ ID NO: 41) is released from the 2H is6NT2 tags by proteolytic cleavage using a protease 3C:fusion protein ratio of 1:100 (w/w) at 4° C. To remove the released 2H is6NT2 tag, the cleavage mixture is loaded onto a second Ni-Sepharose, and the flow through is collected.
Example 21
Production of Green Fluorescent Protein (GFP)
The GFP utilized in this example is a S147P variant, see Kimata, Y et al., Biochem. Biophys. Res. Commun. 232: 69-73 (1997).
A) With NT
An expression vector was constructed comprising a gene encoding NT2-GFP (i.e. NTNT-GFP) as a fusion to His6LinkHis6 (SEQ ID NOS:42-43). The vector was used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that were grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of 0.9-1, induced with IPTG, and further incubated for 3 hours at 25° C. The cells were harvested and resuspended in 20 mM Tris-HCl (pH 8.0).
Lysozyme was added, and the cells were incubated for 30 min on ice. The cells were disrupted by sonication on ice for 5 min, alternating 2 sec on and 2 sec off. The cell lysate was centrifuged at 20 000×g for 30 min. The supernatants were loaded onto a column packed with Ni-Sepharose (GE Healthcare, Uppsala, Sweden). The column was washed extensively before bound proteins were eluted with a 300 mM imidazole. Fractions containing the fusion proteins were pooled and dialyzed against 20 mM Tris-HCl (pH 8.0). The GFP protein (SEQ ID NO: 44) was released from the 2H is6NT2 tags by proteolytic cleavage using a protease 3C:fusion protein ratio of 1:100 (w/w) at 4° C. To remove the released 2H is6NT2 tag, the cleavage mixture was loaded onto a second Ni-Sepharose, and the flow through was collected.
The eluates were subjected to SDS-PAGE on a 12% Tris-Glycine gel under reducing conditions (FIG. 8). Major bands corresponding to the fusion protein (first eluate, left lane) and the target protein (second eluate, right lane) are indicated by the arrows in FIG. 8. The yield was determined by mg purified protein from 1 liter shake flask culture grown to an OD600 of 1. The yield was 44 mg/l of the fusion protein and 16 mg/l of the target protein.
The purified GFP was highly fluorescent, confirming the right fold (beta barrel with linking alpha helix) that is obligate for autocatalytic formation of the chromophore.
B) With Other Purification Tags: Zb and His6ABP (Comparative Example)
BL21(DE3) cells harboring the vectors (pT7ZbGFP, pT7His6ABPGFP) were grown over night at 37° C. in tryptic soy broth media supplemented with kanamycin. On the following morning, the cultures were inoculated into 100 ml fresh media in 1 liter shake flasks and grown until an OD600 of 1 was reached. Protein production was then induced by addition of IPTG to a final concentration of 1 mM, and production continued for 18 h. The cells were harvested and resuspended in 50 mM sodium phosphate buffer (pH 7.5). The cells were disrupted by sonication on ice for 3 min, alternating 1 sec on and 1 sec off. The cell lysate was centrifuged at 10 000×g for 20 min. The supernatants were loaded onto columns.
The ZbGFP (SEQ ID NO: 45) fusion protein was purified on 1 ml HiTrap S HP columns in 50 mM sodium phosphate pH 7.5 and eluated with the same buffer supplemented with 160 mM NaCl.
The His6ABPGFP (SEQ ID NO: 46) fusion protein was purified on 1 ml Talon columns in 50 mM sodium phosphate pH 8 and eluted with the same buffer supplemented with 30 mM acetic acid and 70 mM sodium acetate, which gives a pH of 5.0.
The eluates were subjected to SDS-PAGE on a 10-20% gradient gel under reducing conditions. The yield was determined by mg purified protein/1 liter shake flask culture grown to an OD600 of 1. The yield was 10 mg/l for ZbGFP and 7 mg/l for His6ABPGFP.
Example 22
Production of Neuroserpin
An expression vector was constructed comprising a gene encoding NT2-Neuroserpin (i.e. NTNT-Neuroserpin) as a fusion to His6LinkHis6 (SEQ ID NOS:47-48). The vector was used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences) that were grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of 0.9-1, induced with IPTG, and further incubated for 3 hours at 25° C. The cells were harvested and resuspended in 20 mM Tris-HCl (pH 8.0).
Lysozyme was added, and the cells were incubated for 30 min on ice. The cells were disrupted by sonication on ice for 5 min, alternating 2 sec on and 2 sec off. The cell lysate was centrifuged at 20 000×g for 30 min. The supernatants were loaded onto a column packed with Ni-Sepharose (GE Healthcare, Uppsala, Sweden). The column was washed extensively before bound proteins were eluted with 300 mM imidazole. Fractions containing the fusion proteins were pooled and dialyzed against 20 mM Tris-HCl (pH 8.0).
The neuroserpin protein (SEQ ID NO: 49) was released from the 2H is6NT2 tags by proteolytic cleavage using a protease 3C:fusion protein ratio of 1:100 (w/w) at 4° C. To remove the released 2H is6NT2 tag, the cleavage mixture was loaded onto a second Ni-Sepharose, and the flow through was collected.
The eluates were subjected to SDS-PAGE on a 12% Tris-Glycine gel under reducing conditions (FIG. 9). Major bands corresponding to the fusion protein (first eluate, left lane) and the target protein (second eluate, right lane) are indicated by the arrows in FIG. 9. The yield was determined by mg purified protein from 1 liter shake flask culture grown to an OD600 of 1. The yield was 8 mg/l of the fusionprotein and 4 mg/l of the target protein. As a comparison, the expression yield of neuroserpin with His6 tag was 1.7 mg/l (Belorgey et al. Eur J. Biochem. 271(16):3360-3367 (2004).
The inhibition rate of tPa (tissue plasminogen activator) by the expressed neuroserpin was determined to be the same as published earlier (Belorgey et al. J. Biol. Chem. 277, 17367-17373 (2002).
Example 23
Production of a Protease 3C Fusion Proteins
Expression vectors are constructed comprising a gene encoding His6NT-3C and His6LinkHis6NTNT3C, respectively (Gräslund T. et al., Protein Expr Purif 9(1): 125-132 (1997); Cordingley M G. et al., J. Virol. 63(12): 5037-5045 (1989)). The vectors are used to transform Escherichia coli BL21(DE3) cells (Merck Biosciences), which are grown at 30° C. in Luria-Bertani medium containing kanamycin to an OD600 of 0.9-1, induced with IPTG, and further incubated for 3 h at 25° C. The cells are harvested and resuspended in 20 mM Tris-HCl (pH 8.0).
Lysozyme and DNase are added, and the cells are incubated for 30 min on ice. The cells are further disrupted by sonication on ice for 3 min, alternating 1 sec on and 1 sec off. The cell lysate is centrifuged at 15 000×g for 30 min. The supernatants are loaded onto a column packed with Ni-Sepharose (GE Healthcare, Uppsala, Sweden), equilibrated with 20 mM Tris-HCl (pH 8.0). The column is washed extensively before bound proteins are eluted with 300 mM imidazole. Fractions containing the fusion proteins are pooled and dialyzed against deionized water. The eluate is subjected to SDS-PAGE under reducing conditions. The yield is determined by mg purified protein from 1 liter shake flask culture grown to an OD600 of 1.

## Claims

1. A fusion protein comprising
(i) at least one solubility-enhancing moiety, wherein each solubility-enhancing moiety has at least 90% identity to the amino acid sequence of SEQ ID NO:6; and
(ii) at least one moiety which is a desired non-spidroin protein or a desired non-spidroin polypeptide, wherein the desired non-spidroin protein or the desired non-spidroin polypeptide is selected from the group consisting of amyloid-forming proteins, amyloid-forming polypeptides, surfactant protein B (SP-B), variants of SP-B containing disulphide, apolipoproteins, membrane proteins, membrane polypeptides, protein drugs, polypeptide drugs, aggregation-prone proteins, aggregation-prone polypeptides, and proteases,
wherein the desired non-spidroin protein or the desired non-spidroin polypeptide has less than 30% identity to any of the amino acid sequences of SEQ ID NO: 6-10,
wherein each solubility-enhancing moiety is linked directly or indirectly to the desired non-spidroin protein or the desired non-spidroin polypeptide moiety, and
wherein the desired non-spidroin protein or the desired non-spidroin polypeptide excludes thioredoxin.

2. The fusion protein according to claim 1, wherein each solubility-enhancing moiety contains from 130 to 160 amino acid residues.

3. The fusion protein according to claim 1, wherein the fusion protein comprises at least two solubility-enhancing moieties, each being defined as in claim 1.

4. The fusion protein according to claim 1, wherein the fusion protein comprises at least two consecutive solubility-enhancing moieties, each being defined as in claim 1.

5. The fusion protein according to claim 1, wherein at least one solubility-enhancing moiety is linked directly or indirectly, with intervening sequences selected from linker peptides and/or further solubility-enhancing moieties, to the amino-terminal or the carboxy-terminal end of the at least one desired non-spidroin protein or desired non-spidroin polypeptide moiety.

6. The fusion protein according to claim 5, wherein at least one solubility-enhancing moiety is linked directly or indirectly, with intervening sequences selected from linker peptides and/or further solubility-enhancing moieties, to the amino-terminal end of the at least one desired non-spidroin protein or desired non-spidroin polypeptide moiety.

7. The fusion protein according to claim 5, wherein at least one solubility-enhancing moiety constitutes the amino-tenninal and/or the carboxy-terminal end of the fusion protein.

8. The fusion protein according to claim 1, further comprising
(iii) at least one cleavage site arranged between the at least one desired non-spidroin protein or desired non-spidroin polypeptide moiety and the at least one solubility-enhancing moiety.

9. The fusion protein according to claim 1, comprising a linker which constitutes a handle for identification and purification of the fusion protein.

10. The fusion protein according to claim 1, wherein the desired non-spidroin protein or the desired non-spidroin polypeptide is selected from the group consisting of amyloid beta peptide (Aβ-peptide), islet amyloid polypeptide (IAPP), prion protein (PrP), α-synuclein, calcitonin, prolactin, cystatin, atrial natriuretic factor (ATF) and actin; surface protein B (SP-B), mini-BLeu, α-defensins and β-defensins; class A-H apolipoproteins; (LL-37), surfactant protein C (SP-C), SP-C33, SP-C33Leu, Brichos, GFP, neuroserpin; hormones, including erythropoietin (EPO) and growth hormone (GH), and growth factors, including insulin-like growth factor I (IGF-I) and insulin-like growth factor II (IGF-II); avidin and streptavidin; and protease 3C.

11. The fusion protein according to claim 1, wherein the desired non-spidroin protein or the desired non-spidroin polypeptide is selected from SP-B, mini-B, mini-BLeu, 1a AA, 1b AA, 1a LL and 1b LL, and SP-C, SP-C(Leu), SP-C33, SP-C30, SP-C33(Leu) and KL4.

12. The fusion protein according to claim 11, wherein the desired non-spidroin protein or the desired non-spidroin polypeptide is mini-BLeu.

13. The fusion protein according to claim 11, wherein the desired non-spidroin protein or the desired non-spidroin polypeptide is SP-C33Leu.

14. The fusion protein according to claim 1, selected from the group consisting of the amino acid sequences of SEQ ID NOS 26, 28, 30, 34, 37, 39, 42 and 47; and proteins having at least 95% identity to any one of said amino acid sequences.

15. The fusion protein according to claim 1, wherein the desired non-spidroin protein or the desired non-spidroin polypeptide is selected from the group consisting of amyloid-forming proteins, amyloid-forming polypeptides, surfactant protein B (SP-B), apolipoproteins, membrane proteins, membrane polypeptides, and proteases.

16. The fusion protein according to claim 1, wherein the desired non-spidroin protein or the desired non-spidroin polypeptide is selected from the group consisting of aggregation-prone proteins and aggregation-prone polypeptides, wherein the desired non-spidroin protein or the desired non-spidroin polypeptide excludes thioredoxin.

17. The fusion protein according to claim 1, wherein the desired non-spidroin protein or the desired non-spidroin polypeptide is selected from the group consisting of amyloid beta peptide (Aβ-peptide), islet amyloid polypeptide (IAPP), prion protein (PrP), α-synuclein, calcitonin, prolactin, cystatin, atrial natriuretic factor (ATF) and actin; SP-B, mini-Bleu, α-defensins and β-defensins; class A-H apolipoproteins; (LL-37), surfactant protein C (SP-C), SP-C33, SP-C33Leu, Brichos, GFP, neuroserpin; hormone, insulin-like growth factor I (IGF-I) and insulin-like growth factor II (IGF-II); avidin and streptavidin; and protease 3C.

18. The fusion protein according to claim 17, wherein the hormone is erythropoietin (EPO) or growth hormone (GH).