Methods and Compositions for Protein Expression and Purification
Methods for enhancing expression levels and secretion of heterologous fusion proteins in a host cell are disclosed.
This application is a continuation-in-part of pending U.S. application Ser. No. 10/338,411 filed Jan. 7, 2003 which claims priority to U.S. Provisional Application 60/346,449 entitled “Methods for Protein Expression and Purification” filed Jan. 7, 2002. The entire disclosure of both documents is incorporated by reference herein.FIELD OF THE INVENTION
The present invention relates to the field of recombinant gene expression and purification of expressed proteins. More specifically, the invention provides materials and methods which facilitate purification of heterologous proteins from a variety of different host species.BACKGROUND OF THE INVENTION
Several publications and patent documents are cited throughout the specification in order to describe the state of the art to which this invention pertains. Full citations for those references that are numbered can be found at the end of the specification. Each citation is incorporated herein as though set forth in full.
Functional genomic studies have been hampered by the inability to uniformly express and purify biologically active proteins in heterologous expression systems. Despite the use of identical transcriptional and translational signals in a given expression vector, expressed protein levels have been observed to vary dramatically (5, 7). For this reason, several strategies have been developed to express heterologous proteins in bacteria, yeast, mammalian and insect cells as gene-fusions.
The expression of heterologous genes in bacteria is by far the simplest and most inexpensive means available for research or commercial purposes. However, some heterologous gene products fail to attain their correct three-dimensional conformation in E. coli while others become sequestered in large insoluble aggregates or “inclusion bodies” when overproduced. Major denaturant-induced solubilization methods followed by removal of the denaturant under conditions that favor refolding are often required to produce a reasonable yield of the recombinant protein. Selection of ORFs for structural genomics projects has also shown that only about 20% of the genes expressed in E. coli render proteins that were soluble or correctly folded (36, 38). These numbers are startlingly disappointing especially given that most scientists rely on E. coli for initial attempts to express gene products. Several gene fusion systems such as NUS A, maltose binding protein (MBP), glutathione S transferase (GST), and thioredoxin (TRX) have been developed (17). All of these systems have certain drawbacks, ranging from inefficient expression to inconsistent cleavage from desired structure. Comprehensive data showing that a particular fusion is best for a certain family of proteins is not available.
Ubiquitin and ubiquitin like proteins (UBLs) have been described in the literature. The SUMO system has also been characterized. SUMO (small ubiquitin related modifier) is also known as Sentrin, SMT3, PIC1, GMP1 and UBL1. SUMO and the SUMO pathway are present throughout the eukaryotic kingdom and the proteins are highly conserved from yeast to humans (12, 15, 28). SUMO homologues have also been identified in C. elegans and plants. SUMO has 18% sequence identity with ubiquitin (28, 39). Yeast has only a single SUMO gene, which has also been termed SMT3 (23, 16). The yeast Smt3 gene is essential for viability (29). In contrast to yeast, three members of SUMO have been described in vertebrates: SUMO-1 and close homologues SUMO-2 and SUMO-3. Human SUMO-1, a 101 amino-acid polypeptide, shares 50% sequence identity with human SUMO-1/SUMO-2 (29). Yeast SUMO (SMT3) shares 47% sequence identity with mammalian SUMO-1. Although overall sequence homology between ubiquitin and SUMO is only 18%, structure determination by nuclear magnetic resonance (NMR) reveals that the two proteins share a common three dimensional structure that is characterized by a tightly packed globular fold with D-sheets wrapped around one α-helix(4). Examination of the chaperoning properties of SUMO reveals that attachment of a tightly packed globular structure to N-termini of proteins can act as nucleus for folding and protect the labile protein. All SUMO genes encode precursor proteins with a short C-terminal sequence that extends from the conserved C-terminal Gly-Gly motif. The extension sequence, 2-12 amino acids in length, is different in all cases. Cells contain potent SUMO proteases that remove the C-terminal extensions. The C-terminus of SUMO is conjugated to F amino groups of lysine residues of target proteins. The similarity of the enzymes of the sumoylation pathway to ubiquitin pathway enzymes is remarkable, given the different effects of these two protein modification pathways. Sumoylation of cellular proteins has been proposed to regulate nuclear transport, signal transduction, stress response, and cell cycle progression (29). It is very likely that SUMO chaperones translocation of proteins among various cell compartments, however, the precise mechanistic details of this function of SUMO are not known.
Other fusions promote solubility of partner proteins presumably due to their large size (e.g., NUS A). Fusion of proteins with glutathione S-transferase (GST) or maltose binding protein (MBP) has been proposed to enhance expression and yield of fusion partners. However, enhanced expression is not always observed when GST is used as GST forms dimers and can retard protein solubility. Another problem with GST or other fusion systems is that the desired protein may have to be removed from the fusion. To circumvent this problem, protease sites, such as factor X, thrombin or Tev protease sites are often engineered downstream of the fusion partner. However, incomplete cleavage and inappropriate cleavage within the fusion protein is often observed. The present invention circumvents these problems.SUMMARY OF THE INVENTION
In accordance with the present invention compositions and methods for enhancing expression levels of a protein of interest in a host cell are provided. An exemplary method comprises i) operably linking a nucleic acid sequence encoding molecule selected from the group consisting of SUMO, RUB, HUB, APG8, APG12, URM1, and ISG15 to a nucleic acid sequence encoding said protein of interest thereby generating a construct encoding a fusion protein, ii) introducing said nucleic acid into said host cell, whereby the presence of said molecule in said fusion protein increases the expression level of said protein of interest in said host cell. In a preferred embodiment the molecule is SUMO encoded by a nucleic acid of SEQ ID NO: 2. The method optionally entails cleavage of said fusion protein and isolation of the protein of interest.
In yet another embodiment of the invention, an exemplary method for generating a protein of interest having an altered amino terminus is provided. Such a method comprises i) providing a nucleic acid sequence encoding the protein of interest; ii) altering the N-terminal amino acid coding sequence in the nucleic acid; iii) operably linking a SUMO molecule to the nucleic acid sequence; and iv) expressing the nucleic acid in a eukaryotic cell, thereby producing the protein of interest in the cell, wherein the eukaryotic cell expresses endogenous SUMO cleaving enzymes, which effect cleavage of SUMO from the sequence encoding the protein of interest, thereby producing a protein of interest having an altered amino terminus. All amino acids with the exception of proline may be added to the amino terminus using this method.
The invention also provides a method for producing a sumolated protein for tracking protein localization within a host cell. An exemplary method comprises i) providing a nucleic acid sequence encoding said protein; ii) substituting the N-terminal amino acid coding sequence in the nucleic acid for a codon which encodes proline; iii) operably linking a SUMO molecule to said nucleic acid sequence; and iv) expressing said SUMO linked protein in said host cell.
In another aspect of the invention, a method for enhancing secretion levels of a protein of interest from a host cell is provided. Such a method comprises i) operably linking a nucleic acid sequence encoding molecule selected from the group consisting of SUMO, RUB, HUB, URM1, and ISG15 to a nucleic acid sequence encoding said protein of interest thereby generating a construct encoding a fusion protein, ii) introducing said nucleic acid into said host cell, whereby the presence of said molecule in said fusion protein increases the secretion of said protein of interest from said host cell.
In yet a further aspect of the invention, kits are provided for performing the methods described above. Such kits comprise a recombinant vector containing a nucleic acid sequence encoding a UBL molecule selected from the group of SUMO, RUB, HUB, URM1, and ISG15 operably linked to a promoter suitable for expression in the desired host cell and a multiple cloning site suitable for cloning a nucleic acid encoding the protein of interest. The recombinant vector may also contain a nucleic acid sequence encoding for a purification tag. The kits may further comprise a preparation of a protease capable of cleaving the UBL molecule from the fusion protein, an appropriate solid phase for binding the purification tag, appropriate buffers including wash and cleavage buffers, and frozen stocks of host cells.BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 23 is the amino acid (SEQ ID NO: 1) and nucleotide (SEQ ID NO: 2) sequences of SUMO.
There are a number of reasons for the lack of efficient recombinant protein expression in a host, including, for example, short half life, improper folding or compartmentalization and codon bias. While the Human Genome project has successfully created a DNA “map” of the human genome, the development of protein expression technologies that function uniformly in different expression platforms and for all the protein motifs has not yet been achieved.
In accordance with the present invention, it has been discovered that that N-terminal fusion of the ubiquitin homologue SUMO or Smt3 to otherwise unexpressed or poorly expressed proteins remarkably enhances the expression levels of biologically active proteins in both prokaryotes and eukaryotes. The Ubiquitin-Like protein (UBL) family contains many proteins, including for example, SUMO, Rub1, Hub1, ISGt5, Apg12, Apg8, Urm1, Ana1a and Ana1b (15, 28). See Table 1. The hallmark of all of these proteins, exept APG12, and URM1, is that they are synthesized as precursors and processed by a hydrolase (or proteases) to generate mature carboxy-terminal sequence. Secondly, all of the UBLs share a common structure.
In E. coli, fusion proteins remained intact while in yeast or insect cells fusion proteins were efficiently cleaved, except when proline was the N-terminal residue of the target protein. While any of the UBLs set forth in Table 1 may be utilized in the compositions and methods of the invention to enhance expression of heterologous fusion proteins of interest, SUMO is exemplified in the gene fusion system provided herein.
The SUMO fusion system of the present invention has been successfully applied to express different molecular weight proteins such as 6 KDa Protein G domain to 110 KDa β-galactosidase in E. coli and eukaryotic cells. More specifically, the system allows one to: (1) enhance the expression of under-expressed proteins; (2) increase the solubility of proteins that are insoluble; (3) protect candidate proteins from degradation by intracellular proteases by fusing UBLs to their N-termini; (4) cleave the fusion protein to efficiently generate authentic proteins using naturally-present enzymes (5) generate proteins with novel amino termini; and (6) cleave all fusion proteins with remarkable efficiency irrespective of the N-terminal sequence of the fused protein, using UBL hydrolases such as SUMO hydrolase Ulpl. Because UBLs are small molecular weight proteins (˜100 amino acids), they can also be used as purification tags as well. These remarkable properties of UBLs make them excellent candidates for enhancing expression and solubility of proteins. The method may also be utilized to generate novel amino termini on proteins of interest for a variety of research, diagnostic and therapeutic applications.
The ultimate fate of ubiquitinated or sumoylated proteins within a cell varies. A protein can be monoubiquitinated or polyubiquitinated. Ubiquitination of protein has multiple functions and gives rise to different fates for the protein within a cell (11). Ubiquitination primarily targets proteins to 26S proteosome for degradation (13). On the other hand, sumoylation of target proteins does not lead to degradation, but, rather, leads directly or indirectly to altered localization of proteins (15). There are about 17 deubiquitinating enzymes that cleave conjugated ubiquitin from target proteins as well as ubiquitin-ubiquitin and ubiquitin artificial-fusion proteins (1, 35). Thus far it appears that yeast has two cysteinyl proteases, called Ulp1 and Ulp2, that remove SUMO from ε-amino groups of lysine as well from the artificial linear SUMO-fusions(20, 21).
To determine if UBLs and SUMO fusion will enhance expression of recombinant proteins of different sizes and function, we have designed several UBL-GFP fusion proteins in addition to SUMO-fusion proteins and monitored their expression levels in E. coli, yeast and insect cells. In E. coli, the proteins are expressed as intact fusions, while in eukaryotes, the fusions were efficiently cleaved. A dramatic increase in the yield of proteins after fusion with SUMO and expression in E. coli was observed. In additional studies, SUMO-GFP protein was used as a model fusion for detailed studies in yeast and insect cells. We have designed SUMO-GFP fusion where all the N-terminal methionine residues have been replaced with the rest of the 19 amino acids. We have purified 20 sumo-GFP fusion proteins from E.coli and cleaved them in vitro with Ulp1. Ulp1 efficiently cleaved 19 out of the 20 possible amino acid junctions. The proline junction was not cleaved. As compared to deubiquitinating enzyme (3), Ulp1 demonstrated broad specificity and robustness in its digestion properties. Proteins having a wide range of molecular weights were cleaved efficiently by Ulp1. Similarly, in yeast, and insect cells, the fusion proteins were efficiently processed, yielding intact, biologically active proteins. In addition to enhancing protein expression levels, the SUMO-fusion approach can be used to advantage to generate desired N-termini to study novel N-terminal protein functions in the cell. Since SUMO fusion can both enhance recombinant protein yield and generate new N-termini, this technology provides an important tool for post-genomic biotechnology analyses.
The present invention also encompasses kits for use in effecting enhanced expression, secretion, purification, localization, and alteration of the amino terminus of a protein of interest. Such kits comprise a recombinant vector containing a nucleic acid sequence encoding a UBL molecule selected from the group of SUMO, RUB, HUB, URM1, and ISG15 operably linked to a promoter suitable for expression in the desired host cell and a multiple cloning site suitable for cloning a nucleic acid encoding the protein of interest in-frame with the nucleic acid sequence encoding the UBL molecule. The promoter is preferably a strong promoter and may be constitutive or regulated. Such promoters are well known in the art and include, but are not limited to, the promoters provided hereinbelow such as the ADH1, T7, and CUP1 promoters.
The recombinant vector may also contain a nucleic acid sequence encoding a purification tag in-frame with the sequence encoding the UBL molecule. Purification tags are well known in the art (see Sambrook et al., 2001, Molecular Cloning, Cold Spring Harbor Laboratory) and include, but are not limited to: polyhistidine, glutathione-S-transferase, maltose binding protein, thioredoxin, the FLAG™ epitope, and the c-myc epitope. Materials and methods for the purification of fusion proteins via purification tags are also well known in the art (see Sambrook et al., Novagen catalog, 2002, examples hereinbelow). Reagents including, but not limited to, solid supports capable of binding the purification tag, lysis buffers, wash buffers, and elution buffers may also be included in the kits.
The kits may further comprise a composition comprising a protease or proteases capable of cleaving the UBL molecule from the fusion protein, cleavage buffers, frozen stocks of host cells, and instruction manuals. The kits may also further comprise reagents for altering the nucleic acid encoding a protein of interest to generate amino termini which are different from those native to the wild-type protein. Methods for altering the nucleic acid are well known in the art and include, but are not limited to, site-directed mutagenesis and oligonucleotide-based site-directed mutagenesis (see BD Biosciences Catalog, 2001; Qiagen Catalog, 2001; Ausubel et al., eds., 1995, Current Protocols in Molecular Biology, John Wiley and Sons, Inc.).
As used herein, an “instructional material” includes a publication, a recording, a diagram, or any other medium of expression which can be used to communicate the usefulness of the composition of the invention for performing a method of the invention. The instructional material of the kit of the invention can, for example, be affixed to a container which contains a kit of the invention to be shipped together with a container which contains the kit. Alternatively, the instructional material can be shipped separately from the container with the intention that the instructional material and kit be used cooperatively by the recipient.
The materials and methods set forth below are provided to facilitate the practice of the present invention.
Design and Construction of E. coli Expression Vectors:
The original vector backbone was developed using pET 24d vector from Novagen (see
Construction of Variable His6SUMO-GFP Fusions:
A N-terminal six his-tagged SUMO (fusion vector was constructed as follows. A PCR product was generated with the primers 5′CCATGGGTCATCACCATCATCATCACGGGTCGGACTCAGAAGTCAATC AA-3′ (SEQ ID NO: 40) and 5′-GGATCCGGTCTCAACCTCCAATC TGTTCGCGGTGAG-3′(SEQ ID NO:41) using yeast Smt3 gene (16) as a template (kind gift of Erica Johnson). The PCR fragment was double digested with Nco I and Bam HI, and then ligated into pET24d, which had been similarly digested. It is important to note that the current invention utilizes a variant of the wild type yeast SUMO sequence. The A nucleotide at position 255 has been replaced with a G nucleotide, thus encoding an alanine instead of a threonine (SEQ ID NOS: 1 and 2). The detailed cloning strategy is provided in
Construction of SUMO-Fusion Vectors from pSUMO:
The gene encoding the protein of interest is cloned in frame with the SUMO tag, in the pSUMO vector, by utilizing the encoded Bsa I site. Bsa I belongs to the family of Class IIS restriction enzymes, which recognize non-palindromic sequences, and cleave at a site that is separate from their recognition sequences. The latter trait gives Class IIS enzymes two useful properties. First, when a Class IIS enzyme recognition site is engineered at the end of a primer, the site is cleaved when digested. Second, overhangs created by Class IIS enzymes are template-derived and thus unique. This is in clear contrast to regular Class II restriction enzymes such as EcoRI, which creates an enzyme-defined overhang that will ligate to any EcoRI-digested end. The unique overhangs produced by Class IIS enzymes can be ligated only to their original partner.
It is often preferable to amplify the gene encoding the protein of interest via PCR prior to cloning into the pSUMO vector. The forward primer must contain the additional standard sequence:
5′-GGTCTCAAGGTNNN-3′(SEQ ID NO:44) where GGTCTC is the Bsa I site and NNN is the first codon of the gene encoding the protein of interest. Additional nucleotides are required for the primer to anneal specifically with the gene of interest during the PCR amplification. The reverse primer may contain another restriction enzyme such as Xho I to allow for directional cloning of a gene into pSUMO. Bsa I can also be employed in the reverse primer to simplify cloning steps, for example, in the following primer:
The PCR product can be digested with both Xho I and Bsa I. A digestion reaction containing just the latter enzyme generates a product that would directionally ligate into the pSUMO vector between the Bsa I and Xho I sites of the MCS.
Construction of pSUMO-Protein G Fusion E. coli Expression Vector:
The B2 IgG binding domain (9) from streptococcus G148 protein was synthesized by three synthetic oligonucleotides. The sequence of the gene is 5′-GT CTTAAGA CTA AGA GGT GGC ACG CCG GCG GTG ACC ACC TAT AAA CTG GTG ATT AAC GGC AAA ACC CTG AAA GGC GAA ACC ACC-3′. (SEQ ID NO:46) The 81 bps oligo sequence is 5′-GCC GTT ATC GTT CGC ATA CTG TTT AAA CGC TTT TTC CGC GGT TTC CGC ATC CAC CGC TTT GGT GGT TTC GCC TTT CAG-3′. (SEQ ID NO:47) The 86 pbs oligo sequence is 5′-CAG TAT GCG AAC GAT AAC GGC GTG GAT GGC GTG TGG ACC TAT GAT GAT GCG ACC AAA ACC TTT ACC GTG ACC GAA TAA GGT ACC CC-3′(SEQ ID NO:48). The bolded nucleotides refer to the AfiII and Kpn1 sites that flank the protein G domain. ACG is the first amino acid residue of the domain. The above three oligos were annealed using the Life Technologies protocol. The annealed fragments were extended by Poll enzyme. The resultant gene was PCR amplified by the following oligo primers G1 forward 5′-CTT GTC TTA AGA GGT-3′ (SEQ ID NO:49) and G2 reverse primer 5′-GCT GGG TAC CTT ATT CGG TCA-3′(SEQ ID NO:50). The above protein G gene was cloned at the AfllI and Kpn1 site of the human ubiquitin gene and expressed as ubiquitin-protein G fusion protein in an E. coli pET 22 expression vector (Novagen). The protein G sequence was in turn amplified from the ubiquitin-protein G fusion plasmid by using the primers 5′-GGTCTCAAGGTACGCCGGCGGTGACCACCT-3′(SEQ ID NO:51) and 5′-AAGCTTATTATTCGGTCACGGTAAAGGTTT-3′(SEQ ID NO:52) and inserted in pSUMO to generate pSUMO-protein G expression vector.
Construction of E. coli SUMO-β-Galactosidase Expression Vector.
E. coli β-galctosidase was amplified using pfu (Stratagene) a preparation of genomic DNA from BL21(DE3) (Stratagene) as a template and the primers 5′-GGTCTCAAGGTATGACCATGATTACGGATTCACT-3′ (SEQ ID NO:53) and 5′-AAGCTTATTATTATTATTTTTGACACCAGACC-3′(SEQ ID NO:54). The PCR products were purified and double digested with Bsa I and Hind III. These were then ligated into the vector pET24d6xHisSUMO, which had been similarly digested.
Construction of E. coli pSUMO-Liver X Receptor (LXR) Expression Vector:
The PCR products of the LXR from amino acid residue 189 to the end of the protein that spans the ligand binding domain was digested with BsaI and HindIII and ligated into the pSUMO vector, also digested with BsaI and HindIII.
Construction of E. coli pSUMO-MAPKAP2 Expression Vector:
The fragment of MAPKAP2, encoded in the plasmid pMON45641, was amplified by PCR and cloned into pET24d 6HisSUMO vector by designing PCR primers that flank the sequence shown
Construction of E. coli pSUMO-Tyrosine Kinase Expression Vector:
For the tyrosine kinase, both, the SUMO fusion and unfused expression vectors were designed. As described above the region of kinase was cloned by PCR flanked with BsaI and Hind III sites that were cloned in to similarly digested pSUMO.
Construction of E. coli pSUMO-β-Glucuronidase Expression Vector:
E. coli β-glucuronidase was the kind gift of Ben Glick, University of Chicago) and amplified with the primers
Construction of E. coli SUMO-Hydrolase Expression Vector:
C-terminal His-tagged SUMO hydrolase/protease Ulp(403-621)p (21) (27) as expressed from pET24d in Rosetta(DE3) pLysS (Novagen). The recombinant rotein was purified using Ni-NTA agarose (Qiagen) and buffer exchanged into 20 mM Tris-HCl pH 8.0, 150 mM NaCl and 5 mM β-mercaptoethanol using a PD-10 column (AP Biotech). About 2 ug of the pure protein was analyzed on gels and data shown in
Construction of E. coli UBL-GFP Fusion Vectors.
DNA sequences encoding ubiquitin (Ub), SUMO, Urm1, Hub1, Rub1, Apg8, and Apg12 were PCR-amplified using Deep-Vent polymerase (NEB) and yeast strain DNA to generate a template. Full-length human ISG15 cDNA was a kind gift of Dr. A. Haas, Medical College of Wisconsin, Milwaukee. A unique NcoI site followed by 6His sequence was introduced by PCR at the 5′-end of each Ub1 cDNA. Primer sequence at the 3′-end included unique Esp3I and Hindlll sites. PCR products were digested with NcoI/HindIII and inserted into respective sites of pET24d vector (Novagen) as described above. Full length GFP sequence (Clontech Cat # 60610-1) flanked by Esp3I and HindIII sites, respectively, was PCR-amplified and cloned into pCR4-TOPO-TA vector (Invitrogen). Esp3I/HindIII digested GFP-encoding gene was inserted into respective sites of pET24d-UBLl plasmids, creating final UBL-GFP expression vectors for E. coli. In toto, there were nine plasmid constructs coding for the following structures: 6His-Ubl-GFP. All plasmids were sequenced to confirm the expected structure.
Design and Construction of Yeast UBL-Fusion Vectors:
Saccharomyces cerevisiae has been used as a eukaryotic model for all the experiments involving yeast. All of the expression vectors for these studies were designed on multicopy yeast vectors that contain tryptophan or leucine as a selectable marker and 2μ as an origin of replication(22). Proteins were expressed as unfused products or as ubiquitin, SUMO or other UBL fusion proteins.
Construction of the β-Glucuronidase Yeast Expression Vectors:
To demonstrate that UBLs increase the level of secretion of the protein to the media, in addition to enhancing the level of expression, expression vectors were constructed with and without ubiquitin. We have also compared ubiquitin fusion and SUMO fusion using GFP as a model protein (see
Construction of SUMO-N-GFP Yeast Expression Vector:
To determine what variety of N-terminal variant amino acids at the junction of SUMO and GFP can be cleaved in yeast we designed SUMO-GFP vectors in which all 20 amino acid residues were encoded at the N-terminus of GFP. Essentially all 20 SUMO-X-GFP vectors designed for E. coli expression were digested with Bsa I-Hind III, and the inserts were purified. The 20 inserts were cloned in Yep12 that was slightly modified. Specifically, YeEpSW was generated by digesting Yep12 with Bam HI and Sacd. The CUP1 promoter region was recovered from the fragment by PCR. A polylinker was created at the 3′ end of CUP1 with a variety of restriction sites including NcoI and Xho1. All 20 SUMO-GFPs (N end variants) were digested with NcoI-XhoI enzymes and cloned directly YepSW. The resultant vector YepSW-SUMO-eGFP utilizes tryptophan selection and expresses SUMO-GFP proteins under the control of the copper promoter. All vectors were sequenced to ensure correct codons at the junction of SUMO and GFP.
Construction of UBL-GFP Fusion Yeast Expression Vectors:
Construction of the UBL-GFP fusion vectors for E. coli has been described above. In order to make UBL yeast expression vector NcoI/XhoI fragments carrying GFP alone and all the Upl-GFP fusions were inserted into respective sites of pYEp SW (see above) that was similarly digested with NcoI/XhoI. Insertion of UBL-GFP cassette in Yep SW (See
Design and Construction of Recombinant Baculovirus for SUMO and Ubiquitin GFP Fusion Expression:
To demonstrate that attachment of SUMO or ubiquitin to GFP increases its expression and enhances secretion into the media, several GFP fusion vectors were designed with different configurations of gp67 secretory signals. The basic GFP vector for expression is essentially based on E. coli vectors described above. Derivatives of this vector representing each candidate gene have been constructed by designing PCR primers. The construction of GFP plasmid transfer vectors for baculovirus is described. To help appreciate the rationale for the secretory signal in the context of GFP-fusion, see the diagrammatic representation shown in
(i) pFastbacE. A synthetic oligonucleotide containing the Esp3I site was inserted between BamHI and EcoRI cloning site of the transfer vector pFastbac1, which had been modified by removing Esp3I site from Gmr region. (ii) pFastbacG. The signal sequence of the gp67 gene derived from pACSecG2T was isolated by PCR using 2 primers (f-gp67 and r-gp67), digested with BglII and EcoRI in the next step, and then inserted between BamHI and EcoRI cloning sites of the transfer vector pFastbacE. (iii) pFastbacS. A full-length SUMO gene derived from pET SUMO was generated by PCR using 2 primers (f-bacsmt and r-bacsmt), digested with BsaI and EcoRI in the next step, and then inserted between BamHI and EcoRI cloning sites of the transfer vector pFastbacE. (iv) pFastbacG/S. The signal sequence of the gp67 gene in the pACSecG2T vector was generated by PCR using 2 primers (f-fusgp67 and r-fusgp67), and inserted between BamHI and EcoRI cloning sites of the transfer vector pFastbacE to create a new pFastbacG, which was used for fusion with SUMO afterward. A full-length SUMO gene derived from pET SUMO as described above (iii) was digested with BsaI and SacI and inserted between Esp3I and SacI cloning sites of the new transfer vector pFastbacG. (v) pFastbacS/G. A full-length SUMO gene derived from pET SUMO was generated by PCR using 2 primers (f-fussmt3 and r-fusgp67) and inserted between BamHI and EcoRI cloning sites of the transfer vector pFastbacE to create the new pFastbacS, used for fusion with gp67 afterward. The signal sequence of the gp67 gene derived from pACSecG2T as described above (ii) was digested with BsaI and SacI, and then inserted between the Esp3I and SacI cloning sites of the new transfer vector pFastbacS.
Preparation of Baculovirus Stocks and Cell Growth.
Transfer vector constructs based on the pFastbac 1 shuttle plasmid (Invitrogen, Inc.) were transposed in DH10Bac E. coli competent cells to transfer the respective e-GFP fusion sequences into recombinant virus DNA by site-specific integration. After alkaline lysis of transformed (white colonies) of E. coli cells, which contain recombinant virus (bacmid) DNA, and extraction of the recombinant bacmid DNA, the bacmid DNA was used to transfect Spodoptera frugiperda (Sf9) insect cells, in which virus replication occurs. The virus was then amplified to produce passage 2 (for long-term storage) and passage 3 virus (for working) stocks by infection of fresh Sf9 cell cultures and used directly to infect cells for fusion protein expression. Virus infectivity (pfu/ml) was determined by titration in Sf9 cells using the BacPAK™ Rapid Titer Kit (BD Sciences Clontech, Inc.). A 50 ml culture of Hi-Five cells at concentration of 1×106 cells/ml, was infected with recombinant virus at MOI=5 in Express Five media (serum free media). The cells were grown in 100 ml spinner flask at 27° C. Every 24 hours, cell viability was determined by trypan blue and cell counting. 5ml of the suspension culture was removed at 24 hour intervals, centrifuged at 500×g at 4° C. in 10 minutes. The supernatant was transferred into a fresh tube to monitor any protein that may have been secreted into the media (see below).
Analysis of Proteins from Insect Cell Compartments:
Cell pellets (from above step) were gently washed in 1 ml PBS and recentrifuged at 500×g at 4° C. for 10 minutes. All supernatant and pellets are stored at −80° C. The presence of recombinant protein in cells and media was ascertained by SDS-PAGE and Western blotting of supernatant and cell pellets. The total intracellular protein was extracted by M-PER extraction buffer (Pierce), a neutral buffer for protein extraction. The cell pellet was mixed with rapid pipetting and incubated for 1 hour on an orbital shaker. The suspension was centrifuged at 500×g at 4° C. for 10 minutes to remove debris. The supernatant contained extracted cellular proteins that were either analyzed by PAGE or stored at −80° C. To analyze the proteins present in the media, the following procedure was adopted. Trichloroacetic acid was added to 5 ml media to a final concentration of 20%. The suspension was mixed well and left on ice for three hours, and then centrifuged 500×g at 4° C. for 10 minutes. The white pellet was washed with 80% ethyl alcohol twice, and then dried. The pellet was suspended in 1 ml of M-PER buffer for PAGE to compare the distribution of control (unfused) and SUMO-fused proteins inside and outside the cell.
Methods for Analysis of Yeast Expressed Fusion Proteins:
Yeast cultures were grown in synthetic or rich media. Standard yeast and E. coli media were prepared as described (31). The yeast strain Y4727: Mata his3-Δ200 leu2-Δ0 lys2-Δ0 met5-Δ0 trp1-Δ63 ura3-Δ0 was used as a host (gift from Dr. Jeff Boeke) or BJ 1991. Yeast transformation was performed according to published procedures (8). Yeast transformants with autonomously replicating plasmids were maintained in yeast selective media. The E. coli β-Galactosidase and β-Glucuronidase proteins were expressed under the regulation of either the alcohol dehydrogenase (ADH), or Glyceraldehyde-Phosphate-Dehydrogenase (GPD) promoter or copper metallothioneine (CUP 1) promoter in 2 μm multicopy plasmids with the LEU2 selective marker.
Yeast cells were transformed with appropriate expression vectors, and single colonies were grown in synthetic media minus the selectable marker. For each protein, at least two single colonies were independently analyzed for protein expression. Cells were grown in 5 ml culture overnight and, in the morning, the culture was diluted to an O.D. at 600 nm of 0.5. If the gene was under the control of copper inducible promoter, copper sulfate was added to 100 uM and the culture was allowed to grow for at least three hours. Cells were pelleted at 2000×g for 5 minutes, washed with 10 mM Tris-EDTA buffer pH 7.5. If enzymatic assays were performed, cells were disrupted in assay buffer with glass beads, 2× times the volume of the pellet. Cells were centrifuged and the supernatant was recovered for enzymatic or protein analysis. Alternatively, if the level and the type of protein was analyzed by SDS-PAGE, cell pellet was suspended in SDS-PAGE buffer and boiled for 5 mins. The suspension was centrifuged, and 10-20 ul aliquots were run on 12% SDS-PAGE.
Measurement of β-GUS Activity from Yeast:
β-Glucuronidase (GUS) is a 65 kDa protein that is a useful marker for protein trafficking. We have used GUS to determine the role of N-terminal ubiquitin on secretion of GUS in yeast. Yeast cells were transformed with various GUS vectors, grown overnight in selective liquid media at 30° C., and diluted in the liquid selective media to 0.1 OD600 (OD culture). Yeast cells were incubated in the presence of inducer in shaker at 30° C. Affer 4 hours of incubation, 100 μl of 2× “Z” Sarcosine-ONPG buffer (120 mM Na2HPO4, 80 mM NaH2PO4, 20 mM KCl, 2 mM MgSO4, 100 mM β-mercaptoethanol, pH 7.0, 0.4% lauroyl sarcosine) was added. (The 2× “Z” Sarcosine- buffer is freshly prepared or stored at −20° C. prior use.) We used a fluorometric assay with 4-methylumbelliferyl β-D-glucuronide as the substrate for β-GUS assay. After incubation at 37° C. for 1 hour (t incubation), the reaction was stopped by adding 100 μl of quenching solution, 0.5 M Na2CO3. The GUS activity was determined by reading the plates in a fluorometric plate reader. For calorimetric reactions, relative activity was calculated as following: (1000×OD reaction)/(t incubation×OD culture).
E. coli Growth, Compartmentalization and Protein Expression.
Protein expression studies were carried out in the Rosetta bacterial strain (Novagen). This strain is derived from the lambda DE3 lysogen strain and carries a chromosomal copy of the IPTG inducible T7 RNA polymerase along with tRNAs on a pACYC based plasmid. Cultures were grown in LB as well as minimal media and at growth temperatures of 37° C. and 20° C. with 100 ug/mL ampicillin and 30 ug/mL chloramphenicol. The culture was diluted 50 fold and grown to mid log (OD at 600 nm=0.5-0.7), at which time the culture was induced with 1 mM IPTG. Induction was allowed to proceed for 4-5 hrs, Upon completion of induction, cells were centrifuged and resuspended in a buffer containing 20% sucrose. To analyze protein induction in total cells, SDS-PAGE buffer was added and the protein was analyzed following SDS-PAGE and staining with Coomassie blue.
Separation of Soluble and Insoluble Fractions.
E. coli were harvested by mild centrifugation and washed once with PBS buffer. Cells were resuspended in 4 ml of PBS and ruptured by several pulses of sonication. Unbroken cells were removed by mild centrifugation (5 min at 1500×g) and supernatants were sonicated again to ensure complete cell lysis. An aliquot (5 μl) was mixed with 2% SDS to ensure that no viscosity is detected owing to lysis of unbroken cells. After ensuring that no unbroken cells remained in the lysate, insoluble material consisting of cell walls, inclusion bodies and membrane fragments was sedimented by centrifugation (18,000×g for 10 min). The supernatant was considered “Soluble fraction”.
The pellets were washed from any remaining soluble proteins, lipids and peptidoglycan as follows. Pellets were resuspended in 600 μl of PBS and to the suspensions 600 μl of solution containing 3 M urea and 1% Triton X100 was added. The suspension was briefly vortexed and insoluble material was collected by centrifugation as above. The PBS/Urea/Triton wash was repeated two more times to ensure complete removal of soluble proteins. The washed pellets, designated as “insoluble fraction,” consisted primarily of inclusion bodies formed by over expressed proteins. Approximately I Ofg of protein from each fraction was resolved on 12% SDS-PAGE minigels and stained with Coomassie Brilliant Blue.
Fluorescence (GFP Activity) Assessment.
GFP fluorescence was measured in soluble fractions (approx. 0.1 mg of soluble protein in a final volume of 40 μl) using Fluoroscan Accent FL fluorometer (LabSystems) with Excitation 485 nm/Emission 510 nm filter set with the exposure set to 40 sec. The data are presented in Arbitrary Units (AU).
Twenty μg of total yeast protein per lane were resolved on 12% SDS-PAGE minigel and electro-blotted to nitrocellulose membranes by standard methods. Membranes were blocked with 5% milk in TTBS buffer and incubated with rabbit anti-GFP antibodies (Clontech, cat no. 8367) at 1:100 dilution overnight at 4° C. Secondary HRP-conjugated antibodies were from Amersham. Identical gels were run in parallel and stained with Coomassie to ensure equal loading of the samples.
The various 6HisxSUMO-GFP (16) fusions were expressed in Rosetta(DE3) pLysS (Novagen) using the procedures recommended by the manufacturer. Expression levels in the absence and presence of the fusion proteins was compared by SDS-PAGE analysis. The recombinant proteins were purified using Ni-NTA agarose; (Qiagen) using procedures recommended by the manufacturer.
Cleavage of Proteins
For studies in E. coli, an organism that does not possess SUMO or ubiquitin cleaving enzymes, each cleavage reaction contained 100 ul of purified fusion protein, 99 ul of the buffer 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 5 mM β-mercaptoethanol, and 1 ul of enzyme. The reactions were incubated for 3 hours at 30° C., and stopped by addition of 6× Laemmli SDS-page loading buffer followed by boiling at 95° C. for 5 minutes. The products of the cleavage reaction were analyzed by SDS-PAGE.
The following examples are provided to illustrate various embodiments of the present invention. They are not intended to limit the invention in any way.EXAMPLE I Attachment of C-Terminus of UBLs to N-Terminus of GFP Enhances the Expression and Solubility of the Protein in E. coli
The design and construction of all the UBL E. coli expression vectors has been described above. The DNA sequences, accession numbers of the UBL-GFP fusion proteins, and translation frames are shown
In addition, it is shown that ISG15 plays a role in immune response (24). Thus presentation of ISG15 as a fusion protein is a viable tool for novel vaccine candidates. Similarly, Apg8 and Apg12 translocate protein to compartments in the cell for autophagy (30).
Similar experiments were performed with all the UBL-GFP fusion proteins, but the induction was performed at 26° C. overnight. The data shown in
To gain more insight into the role of UBLs in enhancement of expression and solubility, we have tested the SUMO-fusion systems with other proteins as well. Serine threonine kinases, tyrosine kinase and human nuclear receptor have proven difficult to express in E. coli. Researchers have opted to use tissue culture systems to express soluble kinases of receptors.
Human nuclear receptor proteins, such as steroid receptors, contain ligand-binding domains. These proteins have proven hard to express in soluble form in E. coli. We have used human liver X receptor (LXR) ligand binding domain to demonstrate that SUMO fusion promotes solubility of the protein in E. coli. The ligand-binding domain of LXR was expressed as SUMO fusion in Rosetta plysS cell at 20° C. or 37° C. and the pattern of soluble and insoluble protein was analyzed.
Overall, these results show that in bacteria, fusion of UBLs to GFP increases the level of expression from 2-40 fold. Some of the UBLs such as Ub, SUMO, Urm1, Hub1, and ISG15 solublize otherwise insoluble proteins. In particular, SUMO has been demonstrated to increase solubility of kinases and LXR a under controlled temperature induction from 50-95% of the total expressed protein.EXAMPLE II SUMO-Fusion Expression in Yeast and Insect Cells Fusions of C-Terminal UBLs to the N-Terminus of GFPs are Cleaved in Yeast
To further assess the utility of UBL fusion in eukaryotic cells we expressed all of the UBL-GFP fusions previously described in
Generation of New Amino Termini:
The identity of the N-terminus of a protein has been proposed to control its half-life (the N-end Rule) (35). Many important biopharmaceuticals such as growth factors, chemokines, and other cellular proteins, require desired N-termini for therapeutic activity. It has not been possible to generate desired N-termini, as nature initiates translation from methionine, but the SUMO system offers a novel way to accomplish this.
To demonstrate that all N-termini of GFP in SUMO-GFP fusions were efficiently cleaved when expressed in yeast, a comprehensive study of SUMO-GFP with 20 N-termini was carried out. Multi-copy yeast expression plasmids were designed as described above. Plasmids were transformed in yeast strain BJ 1991, four single colonies were selected, and the levels and cleavage patterns of two of the strains were analyzed by SDS-PAGE and western blotting. Data from Western blots of a single colony is presented in
Previous studies have shown that attachment of ubiquitin to the N-termini of proteins in yeast enhances expression, and protein fusions containing all amino acid at the N-terminal residue, except proline, are efficiently cleaved in yeast (2, 10, 34). However, these technologies have several drawbacks. Firstly, none of the deubiquitinating enzymes (DUBs) have been shown to efficiently cleave ubiquitin fusion proteins of varying sizes and structures (3,1), despite the fact that they were discovered more than 15 years ago (35, 19, 3). Secondly, and perhaps more importantly, ubiquitin predominantly functions as a signal for proteolysis(14). Therefore, for physiological reasons and for the lack of robust cleavage of artificial ubiquitin-fusions by DUBs, the ubiquitin gene fusion system has not been successfully developed for commercial applications. We have observed that the SUMO system appears to perform in a manner that is remarkably superior to that of ubiquitin, as SUMO-and other UBL fusions enhance protein expression and solubility in prokaryotes. In addition, many of the UBLs increase expression of GFP, following the cleavage of UBL in yeast. Unlike the ubiquitin-fusion system, which may direct the protein to the ubiquitin proteosome pathway, the current cleavage of fusion-protein in yeast is the result of C-terminal fusion with SUMO, and proteins generated with novel N-termini are not subject to degradation by the ubiquitin-proteosome pathway. This is one of the reasons that large amount of GFP has accumulated in yeast after cleavage of the SUMO fusion (see
N-terminal Attachment of Ubiquitin Promotes Protein Secretion:
To date, a role for ubiquitin in the secretion of proteins has not been determined. We have assessed whether N-terminal fusion of ubiquitin to a protein promotes its secretion in yeast. Several yeast expression vectors that express E. coli β-glucoronidase (GUS) were designed. All of the yeast GUS expression vectors described in Table 2 are engineered under the control of the strong glycolytic GPD promoter that expresses constitutively. Some of the constructs were also expressed under the control of a copper regulated metallothionein promoter (CUP1) as well. CUP1 promoter driven synthesis of the SUMO-GUS constructs was induced by addition of 100 uM copper sulfate and incubation of 3 hours. To determine the level of GUS from media, cells were harvested by centrifugation at 2000×g for 10 mins. Supernatant was collected and equal amounts of aliquots were assayed for enzymatic activity or western blot analysis as described above. For the comparative study, all strains were treated identically and grown at the same time to equal O.D, and the assays were performed at the same time. To examine intracellular enzymatic activity, the cells were harvested by centrifugation and washed with Tris EDTA buffer, pH 7.5. The cell pellets were suspended in sarcosine buffer and ruptured with glass beads at 4° C., three times by vigorously vortexing. Supernatant was collected for assay of the enzymatic activity. The amount of protein secretion was determined by estimating relative activity of the enzyme in the media. The data is shown in Table 2.
GUS activity was measured as described. It was not possible to measure specific units of GUS in the media as yeast grown in synthetic media. Yeast secretes little protein and current methods of protein estimation, BioRad kit cannot estimate the protein, the data was presented as + where one + is equal to 2 units of GUS as described in invention. − Sign means no GUS activity was detected.
The following conclusions are drawn from this study.
- 1) Fusion of ubiquitin to GUS leads to a several fold increase when yeast extracts were analyzed by enzymatic assays.
- 2) Insertion of proline at the junction of ubiquitin and GUS did not allow cleavage of the ubiquitin-GUS fusion protein.
- 3) The attachment of alpha factor secretory sequences to the N-terminus of ubiquitin-fusion did not have show any appreciable increase in secretion of the protein into the media.
- 4) Presence of alpha factor sequences between ubiquitin and GUS did not lead to any increase in extracellular level of GUS activity.
- 5) Greatest amount of secretion was observed with ubiquitin-Met-GUS. These observations suggest that endogenous secretory sequences of GUS in the context of ubiquitin promote the best secretion for GUS. To this end the current data from yeast correlates very well with the ubiquitin-GFP protein secretion in insect cells (see
Fusion of SUMO and Ubiquitin to the N-Terminus of GFP Promotes Enhanced Expression and Secretion in Insect Cells.
The role of SUMO in enhanced expression and secretion of proteins in cultured cells has also been studied in insect cells. Baculovirus vectors expressing SUMO-GFP constructs and appropriate controls have been described above. See
Similar experiments were performed with cells 48 hours post infection. The data in
We have also discovered that SUMO-Pro-GFP fusion was not cleaved by endogenous SUMO hydrolases in insect cells (
Further confirmation of these observations was obtained by fluorescence imaging of the cells expressing GFP fusion proteins.
- 1) The increase in the amount of SUMO-fusion protein expression in insect cells was several-fold higher (20-40 fold) than that of unfused protein, as determined by and Western blot analysis.
- 2) All of the SUMO-GFP constructs that contain methionine at the +1 position were cleaved except SUMO-Proline-GUS. This aspect of the SUMO-fusion technology allows us to express proteins that are stably sumoylated.
- 3) Attachment of ubiquitin to the N-terminus of GFP led to dramatic enhancement in secretion of the protein in the media. Ubiquitin promotes secretion of proteins that may or may not have endogenous secretory signal. Thus, N-terminal ubiquitination may be utilized as a tool to enhance secretetion of proteins in eukaryotic cells.
- 4) N-terminal SUMO also promotes secretion of protein in insect cells.
SUMO Protease ULP1 Cleaves a Variety of SUMO-Fusion Proteins:
Properties and Applications in Protein and Peptide Expression and Purification
Yeast cells contain two SUMO proteases, Ulp1 and Ulp2, which cleave sumoylated proteins in the cell. At least eight SUMO hydrolases have been identified in mammalian systems. The yeast SUMO hydrolase Ulp1 catalyzes two reactions. It processes full length SUMO into its mature form and it also de-conjugates SUMO from side chain lysines of target proteins. Examples I and II establish our findings that attachment of SUMO to the N-terminus of under-expressed proteins dramatically enhances their expression in E. coli, yeast and insect cells. To broaden the application of SUMO fusion technology as a tool for expression of proteins and peptides of different sizes and structures, the ability of Ulp1 to cleave a variety of proteins and peptides has been examined. Purified recombinant SUMO-GFPs were efficiently cleaved when any amino acid except Proline is present in the +1 position of the cleavage site. Similar properties of SUMO hydrolase Ulp1 were observed when Sumo-tyrosine kinase, Sumo-protein G, Sumo-β-GUS, and SUMO MAPKAP2 kinase were used as substrates. The in vitro activity of the enzyme showed that it was active under broad ranges of pH, temperature, and salt and imidazole concentration. These findings suggest that the Ulp1 is much more robust in cleavage of the SUMO-fusion proteins as compared to its counterpart, ubiquitin-fusion hydrolase. Broad specificity and highly efficient cleavage properties of the Ulp1 indicate that SUMO-fusion technology can be used as a universal tag to purify a variety of proteins and peptides, which are readily cleaved to render highly pure proteins.
The following materials and methods are provided to facilitate the practice of Example III.
Affinity Purification and Cleavage of SUMO Fusion Proteins with SUMO Hydrolase.
The following table lists the solutions required for the affinity purification and cleavage procedures:
From typical 250 ml cultures, the samples are pelleted by centrifugation, and supernatants are removed by decanting. Generally, from 250 ml of culture, 1.0 -1.5 grams of wet cells are produced. Pelleted cells are then resuspended in 5-10 ml of lysis buffer. RNase and DNase are added to final concentration of 10 ug/ml lysis solution. Samples are kept on ice throughout the sonication procedure. Using an appropriate tip, the samples are sonicated 3 - 5 times for 10 second pulses at 50% duty cycle. Sonicates are incubated on ice for 30 minutes; if the samples are viscous after this time, the sonication procedure is repeated. Lysed samples (in lysis solution) are loaded onto 1-ml columns. The columns are washed with 5 to 10 volumes of wash buffer (wash fractions are saved until the procedure is complete). Columns are developed with 2.5 ml of elution buffer, and SUMO hydrolase cleavage is performed by one of two methods: 1) cleavage is performed in elution buffer, with SUMO hydrolase added at 50 ul/250 ml buffer, samples incubated at room temperature for 2 hr or overnight at 4° C., and cleavage monitored by gel electrophoresis; 2) imidazole is first removed by dialysis, gel filtration, or desalting, samples are then resuspended in SUMO hydrolase cleavage buffer, SUMO hydrolase is added at 50 ul/2.5 ml buffer, and samples are incubated at room temperature for 2 hr or at 4° C. overnight, with cleavage monitored by gel electrophoresis. Units of SUMO hydrolase are defined as the amount of enzyme that cleaves 1 ug of pure SUMO-Met-GFP (up to 95%) in 50 mM Tris-HCl pH 8.0, 0.5 mM DTT, 150 mM NaCl at room temperature in 60 minutes.
After cleavage, protein can be stored at 4° C., or subjected to purification.
The expression and purification of carboxy terminus of Ulp1p is described above.
The various His6smt3XeGFP fusions were expressed in Rosetta (DE3) pLysS (Novagen). The recombinant proteins were purified using Ni-NTA agarose (Qiagen). The comparative in vitro cleavage reactions were carried out by first normalizing the amount of the various fusions in each reaction. This was done by measuring the fluorescence properties of the purified fusion proteins using the fluorimeter Fluoriskan II (Lab Systems) and then diluting the more concentrated samples with the Ni-NTA agarose elution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl 300 mM Imidazole and 5 mM beta-mercaptoethanol), such that their fluorescence values equaled that of the lowest yielder. Each cleavage reaction contained 100 ul of protein, 99 ul of the buffer 20 mM Tris-HCl pH 8.0, 150 mM NaCl and 5 mM beta-mercaptoethanol and 1 ul of enzyme. The reactions were incubated for 3 hours at 30° C. after which they were stopped by addition of 6× Laemmli SDS-page loading buffer followed by boiling at 95° C. for 5 minutes. The products of the cleavage reaction were analyzed by SDS-PAGE.
Proline cleavage experiments were carried out in a fashion similar to those described above. The purified His6smt3PeGFP was buffer exchanged into 20 mM Tris-HCl pH 8.0, 150 mM NaCl and 5 mM beta-mercaptoethanol using a PD-10 column. A 10 fold increase in the amount of Ulp1 were added to each reaction. Digestions were incubated for 3 hours at 30° C. All reactions were stopped by addition of Laemmli loading buffer and analyzed by SDS-page.
Conjugation of ubiquitin and SUMO to its target proteins is a highly regulated and dynamic process. Several deubiquitinating enzymes (DUBs) have been identified in yeast and other eukaryotic cells(1). Yeast genetics studies show that many of these enzymes are not essential suggesting that an overlapping function is performed by most of these enzymes. DUBs have been most extensively studied and shown to cleave linear ubiquitin fusions as well isopepetide bonds (3, 35). Much less is known about the enzymes that remove SUMO from isopeptide bonds or artificial SUMO-fusion proteins. Hochstrasser and Li have shown that Ulp1 and Ulp2 remove Smt3 and SUMO 1 from proteins and play a role in progression through the G2IM phase and recovery of cells from checkpoint arrest, respectively(20, 21). Ulp1 and Ulp2 cleave C-terminus of SUMO (-GGATY; SEQ ID NO: 59) to mature form (-GG) and de-conjugate Smt3 from the side chains of lysines(20, 21). The sequence similarity of two enzymes is restricted to a 200-amino acid sequence called ULP that contains the catalytically active region. The three-dimensional structure of the ULP domain from Ulp1 has been determined in a complex form with SUMO (Smt3) precursor(27). These studies show that conserved surfaces of SUMO determine the processing and de-conjugation of SUMO. Database searches of the human genome and recent findings suggest that there are at least 7 human ULPs with the size ranging from 238 to 1112 amino acid residues (18, 33, 39). It is intriguing to note that SUMO Ulps are not related to DUBs, suggesting that SUMO Ulps evolved separately from DUBs. The findings that ULP structure is distantly related to adenovirus processing protease, intracellular pathogen Chlammydia trachomatis and other proposed bacterial cystiene protease core domains suggest that this sequence evolved in prokaryotes(20, 21). Detailed properties of the SUMO proteases are provided in described in Table 3.
Ulp1 has proven extremely robust in cleaving a variety of SUMO-fusion proteins expressed in E. coli as described in the present example. We have designed SUMO-GFP fusions in which the N-terminal methionine has been replaced with rest of the 19 amino acids. Attachment of 6× His to N-terminus of SUMO afforded easy purification of the 20 SUMO-GFP fusions from E. coli. The enzyme was active under broad ranges of pH, temperature, salts and imidazole concentration and was very effective in cleaving variety of proteins from SUMO fusion that includes BPTI a 6.49 KDa, Protein G a 7 KDa, β-Glucuronidase (GUS) and 110 KDa β-Galactosidase (GAL) genes. These findings suggest that the Ulp1 is much more robust in cleavage of the SUMO-fusion proteins as compared to its counterpart ubiquitin-fusion hydrolase.
The effects of various additives/conditions and temperature upon the in vitro cleavage reaction were determined as follows: His6smt3MeGFP was expressed from pET24d in Rosetta(DE3) pLysS (Novagen). The recombinant protein was purified as before using Ni-NTA agarose (Qiagen) and then buffer exchanged into 20 mM Tris-HCl pH 8.0, 150 mM NaCl and 5 mM β-mercaptoethanol using a PD-column (AP Biotech). Cleavage reactions were performed with 100 ug of the purified protein, 0.5 ul of enzyme, the appropriate amount of a stock solution of additive to generate the final concentrations listed in Table 4, plus the exchange buffer up to a final volume of 200 ul. Reactions were incubated for 1 hour at 37° C. except for those at 4° C. were incubated for 3 hours. The data in
The SUMO hydrolase also functions under broad pH range.
As discussed above, for broad utility of the system it is important that the enzyme be able to cleave fusion proteins of different sizes and structures in vitro.
Among dozens of proteins expressed as SUMO fusions in our lab, only one, β-GUS, proved partially resistant to cleavage by the hydrolase. Configurations of artificial SUMO fusion are bound to occur wherein the structure of the protein will hinder the ability of the enzyme to recognize and bind the cleavage site of the fusion protein. This problem has been solved by adding small concentrations of urea, which does not inhibit the hydrolase, but results in cleavage the fusion that was previously resistant.
We have discovered that, due to the rapid folding properties of SUMO, the fused protein can also be rapidly re-natured after treatment of the crude protein mix with chaotropic agents such as guanidinium hydrochloride or urea. We have developed a simple and rapid procedure to purify SUMO-fused proteins that are expressed in prokaryotes and eukaryotes. This method was tested with SUMO-protein G fusion expressed in E. coli. Cells expressing 6×His-SUMO-G protein fusion were harvested and frozen until required for protein purification. Three times the weight per volume lysis buffer (6 M Guanidinium Chloride, 20 mM Tris-HCl, 150 mM NaCl, pH 8.0) was added to the cell pellet rapidly lyse the cells. The supernatant was loaded onto a pre-equilibrated column containing Ni-NTA agarose (Qiagen), the flow through was collected for analysis. The column was then washed, first with 2 column volumes (CV) of Lysis buffer, followed by 3 CV of wash buffer (20 mM Tris-HCl, 150 mM NaCl 15 mM Imidazole pH 8.0). The fusion protein was then eluted using 2 CV of elution buffer (20 mM Tris-HCl, 150 mM NaCl 300 mM Imidazole pH 8.0). The purified product is present in a native buffer that allows for cleavage and release of the peptide from the Sumo fusion using Ulp1. See
- 1. Amerik, A. Y., S. J. Li, and M. Hochstrasser. 2000. Analysis of the deubiquitinating enzymes of the yeast Saccharomyces cerevisiae. Biol Chem 381:981-92.
- 2. Bachmair, A., D. Finley, and A. Varshavsky. 1986. In vivo half-life of a protein is a function of its amino-terminal residue. Science 234:179-86.
- 3. Baker, R. T. 1996. Protein expression using ubiquitin fusion and cleavage. Curr Opin Biotechnol 7:541-6.
- 4. Bayer, P., A. Arndt, S. Metzger, R. Mahajan, F. Melchior, R. Jaenicke, and J. Becker. 1998. Structure determination of the small ubiquitin-related modifier SUMO-1. J Mol Biol 280:275-86.
- 5. Butt, T. R., S. Jonnalagadda, B. P. Monia, E. J. Sternberg, J. A. Marsh, J. M. Stadel, D. J. Ecker, and S. T. Crooke. 1989. Ubiquitin fusion augments the yield of cloned gene products in Escherichia coli. Proc Natl Acad Sci U S A 86:2540-4.
- 6. Butt, T. R., E. J. Sternberg, J. A. Gorman, P. Clark, D. Hamer, M. Rosenberg, and S. T. Crooke. 1984. Copper metallothionein of yeast, structure of the gene, and regulation of expression. Proc Natl Acad Sci U S A 81:3332-6.
- 7. Ecker, D. J., J. M. Stadel, T. R. Butt, J. A. Marsh, B. P. Monia, D. A. Powers, J. A. Gorman, P. E. Clark, F. Warren, A. Shatzman, and et al. 1989. Increasing gene expression in yeast by fusion to ubiquitin. J Biol Chem 264:7715-9.
- 8. Gietz, D., A. St. Jean, R. A. Woods, and R. H. Schiestl. 1992. Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res 20:1425.
- 9. Goward, C. R., J. P. Murphy, T. Atkinson, and D. A. Barstow. 1990. Expression and purification of a truncated recombinant streptococcal protein G. Biochem J 267:171-7.
- 10. Graumann, K., J. L. Wittliff, W. Raffelsberger, L. Miles, A. Jungbauer, and T. R. Butt. 1996. Structural and functional analysis of N-terminal point mutants of the human estrogen receptor. J Steroid Biochem Mol Biol 57:293-300.
- 11. Hicke, L. 1997. Ubiquitin-dependent internalization and down-regulation of plasma membrane proteins. Faseb J 11:1215-26.
- 12. Hochstrasser, M. 2000. Evolution and function of ubiquitin-like protein-conjugation systems. Nat Cell Biol 2:E153-7.
- 13. Hochstrasser, M. 1995. Ubiquitin, proteasomes, and the regulation of intracellular protein degradation. Curr Opin Cell Biol 7:215-23.
- 14. Hochstrasser, M. 1996. Ubiquitin-dependent protein degradation. Annu Rev Genet 30:405-39.
- 15. Jentsch, S., and G. Pyrowolakis. 2000. Ubiquitin and its kin: how close are the family ties? Trends Cell Biol 10:335-42.—00001785—00001785.
- 16. Johnson, E. S., I. Schwienhorst, R. J. Dohmen, and G. Blobel. 1997. The ubiquitin-like protein Smt3p is activated for conjugation to other proteins by an Aos1p/Uba2p heterodimer. Embo J 16:5509-19.
- 17. Kapust, R. B., and D. S. Waugh. 1999. Escherichia coli maltose-binding protein is uncommonly effective at promoting the solubility of polypeptides to which it is fused. Protein Sci 8:1668-74.
- 18. Kim, K. I., S. H. Baek, Y. J. Jeon, S. Nishimori, T. Suzuki, S. Uchida, N. Shimbara, H. Saitoh, K. Tanaka, and C. H. Chung. 2000. A new SUMO-1-specific protease, SUSP1, that is highly expressed in reproductive organs. J Biol Chem 275:14102-6.
- 19. LaBean, T. H., S. A. Kauffman, and T. R. Butt. 1995. Libraries of random-sequence polypeptides produced with high yield as carboxy-terminal fusions with ubiquitin. Mol Divers 1:29-38.
- 20. Li, S. J., and M. Hochstrasser. 1999. A new protease required for cell-cycle progression in yeast. Nature 398:246-51.
- 21. Li, S. J., and M. Hochstrasser. 2000. The yeast ULP2 (SMT4) gene encodes a novel protease specific for the ubiquitin-like Smt3 protein. Mol Cell Biol 20:2367-77.
- 22. Lyttle, C. R., P. Damian-Matsumura, H. Juui, and T. R. Butt. 1992. Human estrogen receptor regulation in a yeast model system and studies on receptor agonists and antagonists. J Steroid Biochem Mol Biol 42:677-85.
- 23. Mahajan, R., L. Gerace, and F. Melchior. 1998. Molecular characterization of the SUMO-1 modification of RanGAP1 and its role in nuclear envelope association. J Cell Biol 140:259-70.
- 24. Malakhova, O., M. Malakhov, C. Hetherington, and D. E. Zhang. 2002. Lipopolysaccharide activates the expression of ISG15-specific protease UBP43 via interferon regulatory factor 3. J Biol Chem 277:14703-11.
- 25. Marathe, S. V., and J. E. McEwen. 1995. Vectors with the gus reporter gene for identifying and quantitating promoter regions in Saccharomyces cerevisiae. Gene 154:105-7.
- 26. Matunis, M. J., J. Wu, and G. Blobel. 1998. SUMO-1 modification and its role in targeting the Ran GTPase-activating protein, RanGAP1, to the nuclear pore complex. J Cell Biol 140:499-509.
- 27. Mossessova, E., and C. D. Lima. 2000. Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. Mol Cell 5:865-76.
- 28. Muller, S., C. Hoege, G. Pyrowolakis, and S. Jentsch. 2001. SUMO, ubiquitin's mysterious cousin. Nat Rev Mol Cell Biol 2:202-10.
- 29. Muller, S., M. J. Matunis, and A. Dejean. 1998. Conjugation with the ubiquitin-related modifier SUMO-1 regulates the partitioning of PML within the nucleus. Embo J 17:61-70.
- 30. Ohsumi, Y. 2001. Molecular dissection of autophagy: two ubiquitin-like systems. Nat Rev Mol Cell Biol 2:211-6.
- 31. Sherman, F., G. Fink, and J. Hicks. 1986. Methods in yeas genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
- 32. Sikorski, R. S., and P. Hieter. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19-27.
- 33. Suzuki, T., A. Ichiyama, H. Saitoh, T. Kawakami, M. Omata, C. H. Chung, M. Kimura, N. Shimbara, and K. Tanaka. 1999. A new 30-kDa ubiquitin-related SUMO-1 hydrolase from bovine brain. J Biol Chem 274:31131-4.
- 34. Varshavsky, A. 1996. The N-end rule: functions, mysteries, uses. Proc Natl Acad Sci U S A 93:12142-9.
- 35. Varshavsky, A. 2000. Ubiquitin fusion technique and its descendants. Methods Enzymol 327:578-93.
- 36. Waldo, G. S., B. M. Standish, J. Berendzen, and T. C. Terwilliger. 1999. Rapid protein-folding assay using green fluorescent protein. Nat Biotechnol 17:691-5.
- 37. Walfish, P. G., T. Yoganathan, Y. F. Yang, H. Hong, T. R. Butt, and M. R. Stallcup. 1997. Yeast hormone response element assays detect and characterize GRIP1 coactivator-dependent activation of transcription by thyroid and retinoid nuclear receptors. Proc Nati Acad Sci U S A 94:3697-702.
- 38. Wright, L. C., J. Seybold, A. Robichaud, I. M. Adcock, and P. J. Barnes. 1998. Phosphodiesterase expression in human epithelial cells. Am J Physiol 275:L694-700.
- 39. Yeh, E. T., L. Gong, and T. Kamitani. 2000. Ubiquitin-like proteins: new wines in new bottles. Gene 248:1-14.
While certain of the preferred embodiments of the present invention have been described and specifically exemplified above, it is not intended that the invention be limited to such embodiments. Various modifications may be made thereto without departing from the scope and spirit of the present invention, as set forth in the following claims.
1. A kit comprising a recombinant vector containing a nucleic acid sequence encoding a UBL molecule selected from the group of SUMO, RUB, HUB, URM1, and ISG15 operably linked to a promoter suitable for expression in the desired host cell and a multiple cloning site suitable for cloning a nucleic acid encoding the protein of interest in-frame with the nucleic acid sequence encoding the UBL molecule.
2. The kit of claim 1, wherein said kit further comprises host cells suitable for expression of said vector.
3. The kit of claim 2, wherein said host cells are selected from the group of yeast cells, E. coli, insect cells, and mammalian cells.
4. The kit of claim 1, wherein said kit further comprises a kit which comprises reagents for altering the nucleic acid encoding said protein of interest to generate amino termini which are different from those native to the wild-type protein.
5. The kit of claim 4, wherein said kit comprises reagents suitable for site-directed mutagenesis.
6. The kit of claim 5, wherein said kit comprises oligonucleotides for performing oligonucleotide-based site-directed mutagenesis.
7. A kit for purification of a protein from a host cell comprising:
- i) a recombinant vector containing a nucleic acid sequence encoding a UBL molecule selected from the group of SUMO, RUB, HUB, URM1, and ISG15 operably linked to a promoter suitable for expression in the desired host cell, a nucleic acid sequence encoding for a purification tag in-frame with the nucleic acid sequence encoding the UBL molecule, and a multiple cloning site suitable for cloning a nucleic acid encoding the protein of interest in-frame with the nucleic acid sequence encoding the UBL molecule, and
- ii) a protease composition capable of cleaving the UBL molecule from the fusion protein.
8. The kit of claim 7, wherein said kit further comprises host cells suitable for expression of said vector.
9. The kit of claim 8 wherein said host cell is selected from the group of yeast cells, E. coli, insect cells, and mammalian cells.
10. The kit of claim 7 further comprising:
- i) a solid support for binding the purification tag,
- ii) lysis buffers,
- iii) wash buffers,
- iv) elution buffers,
- v) cleavage buffers, and
- vi) instruction material.
International Classification: C12N 5/00 (20060101); C12N 1/16 (20060101); C12N 1/20 (20060101); C12N 9/14 (20060101); C12N 15/63 (20060101);