Fusion tags for protein solubility, purification and immunogenicity in Escherichia coli: the novel Fh8 system

1Proteins are key elements of life, constituting the major part of the living cell. They play important roles in a variety of cell processes, including cell signaling, immune responses, cell adhesion, and the cell cycle, and their failure is consequently correlated with several diseases.

2With the introduction of the DNA recombinant technology in the 1970s, proteins started to be expressed in several host organisms resulting in a faster and easier process compared to their natural sources. Escherichia coli remains the dominant host for producing recombinant proteins, owing to its advantageous fast and inexpensive, and high yield protein production, together with the well-characterized genetics and variety of available molecular tools.

3The recombinant protein production in E. coli has greatly contributed for several structural studies; for instance, about 90% of the structures available in the Protein Data Bank were determined on proteins produced in E. coli.. The E. coli recombinant production has also boosted the biopharmaceutical industry: 30% of the recombinant biopharmaceuticals licensed up to 2011 by the U.S. Food and Drug Administration (FDA) and European Medicines Agency (EMEA) were obtained using this host cell.

4Escherichia coli recombinant protein-based products can also be found in major sectors of the enzyme industry and the agricultural industry with applications ranging from catalysis (e.g., washing detergents) and therapeutic use (e.g., vaccine development) to functional analysis and structure determination (e.g., crystallography; ).

5As a bacterial system, the E. coli has, however, limitations at expressing more complex proteins due to the lack of sophisticated machinery to perform posttranslational modifications, resulting in poor solubility of the protein of interest that are produced as inclusion bodies. Previous studies reported that up to 75% of human proteins are successfully expressed in E. coli but only 25% are produced in an active soluble form using this host system. Other problems found within this host system include proper formation of disulfide bonds, absence of chaperones for the correct folding, and the miss-match between the codon usage of the host cell and the protein of interest. Moreover, the industrial culture of E. coli leads cells to grow in harsh conditions, resulting in cell physiology deterioration.

6Despite the above-mentioned issues of E. coli recombinant protein production, the benefits of cost and ease of use and scale make it essential to design new strategies directed for recombinant soluble protein production in this host cell. Several strategies have been made for efficient production of proteins in E. coli, namely, the use of different mutated host strains, co-production of chaperones and foldases, lowering cultivation temperatures, and addition of a fusion partner. The combination of some of these strategies has improved the soluble production of recombinant proteins in E. coli, but the prediction of robust soluble protein production processes is still a “a challenge and a necessity”.

7Nowadays, with the aid of genetic and protein engineering, novel tailor-made strategies can be designed to suit user or process requirements.

8This review describes the key solubility factors that correlate with successful protein production in E. coli, and it presents a comprehensive summary of the available fusion partners for protein production and purification in the bacterial host. A main focus is given to the novel Fh8 fusion system (Hitag®) for soluble protein production, purification and immunogenicity in E. coli.

9The production of recombinant proteins requires a successful correlation between the gene’s expression, protein solubility, and its purification. The production levels of recombinant proteins synthesized in E. coli are no longer pointed as a limitation for the success of the overall process, but care should be taken with the protein solubility, which is still a major bottleneck in the field. The downstream processing is deeply associated with an efficient protein production strategy, and thus it must be tailor-designed to maximize the recovery of pure recombinant proteins.

10All these three properties – expression, solubility, and purification – shall always be considered together as determinants for the effective protein production in E. coli. Several aspects are though essential for each individual success, as resumed in Figure 1 and described.

11Escherichia coli recombinant protein production systems are designed to achieve a high accumulation of soluble protein product in the bacterial cell. However, a strong and rapid protein production can lead to stressful situations for the host cell, resulting in protein misfolding in vivo, and consequent aggregation into inclusion bodies. For instance, macromolecular crowding of proteins at high concentrations in the E. coli cytoplasm often impairs the correct folding of proteins, leading to the formation of folding intermediates that, when inefficiently processed by molecular chaperones, promote inclusion body formation.

12Strategies that direct the soluble production of proteins in E. coli are, thus, envisaged, and become more attractive than protein refolding procedures from inclusion bodies.

13Several methods have been shown to prevent or decrease protein aggregation during protein production in E. coli on a trial-and-error basis, including:

14(i) Lower expression temperatures: bacteria cultivation at reduced temperatures is often used to reduce protein aggregation, since it slows down the rate of protein synthesis and folding kinetics, decreasing the hydrophobic interactions that are involved in protein self-aggregation. Low cultivation temperatures can also reduce or impair protein degradation due to a poor activity of heat shock proteases that are usually induced during protein overproduction in E. coli. This strategy has, however, some drawbacks as the reduction of temperature can also affect replication, transcription, and translation rates, besides decreasing the bacterial growth and protein production yields. Nevertheless, these limitations can be circumvented by the use of cold-inducible promoters that maximize protein production under low temperature conditions.

15(ii) E. coli-engineered host strains: E. coli mutant strains are a significant advance toward the soluble production of difficult recombinant proteins. Several targeted strain strategies have been developed through the introduction of DNA mutations that affect protein synthesis, degradation, secretion, or folding (reviewed in ), including: engineered strains for improved protein processing at low temperatures, such as the Arctic Express strain (Agilent Technologies); mutated strains that increase mRNA stability by attenuation of RNases activity, which is responsible for the shorter half-life of mRNA in E. coli cells; engineered strains that supply extra copies of rare tRNAs, such as the Rosetta strains (Invitrogen) and the BL21 Codon Plus strains (Novagen;; ); mutant strains that facilitate disulfide bond formation and protein folding in the E. coli cytoplasm by render it oxidizing due to mutations in glutathione reductase (gor) and thioredoxin reductase (trxB) genes, and/or by co-production of Dsb proteins, such as the Origami strains (Novagen) or the new SHuffle strain (New England Biolabs; ); and C41 and C43 (Avidis) BL21 (DE3) mutant strains that improve the synthesis of membrane proteins.

16(iii) Cultivation conditions: protein production can be efficiently improved by the use of high cell-density culture systems like batch, which offers a limited control of the cell growth, and fed-batch, which allows the real time optimization of growth conditions. The composition of the cell growth medium and the fermentation variables such as temperature, pH, induction time, and inducer concentration are also essential for the prevention of protein aggregation, whereby a careful optimization improves the yield and quality of soluble protein production.

17(iv) Co-production of molecular chaperones and folding modulators: the initial folding of proteins can be assisted by molecular chaperones that prevent protein aggregation through binding exposed hydrophobic patches on unfolded, partially folded or misfolded polypeptides, and traffic molecules to their subcellular destination. Protein aggregation is also prevented by folding catalysts that catalyze important events in protein folding such as the disulfide bond formation. A low concentration of these folding modulators in the cell often results in protein folding failures; thereby their co-production together with the target protein becomes a suitable strategy for the improvement of soluble protein production in E. coli (reviewed in;;;;;; ). Chaperones like trigger factor, DnaK, GroEL, members of the heat shock protein Hsp70 and Hsp60 families (hsHsp proteins), and ClpB assist protein folding in the E. coli cytoplasm, and their individual or cooperative activities presents different contributions for target protein solubility.

18(v) Fusion partner proteins: in contrast to the above-mentioned strategies, the use of fusion partners involves the target protein engineering. Fusion partners are very stable peptide or protein molecules soluble expressed in E. coli that are genetically linked with target proteins to mediate their solubility and purification.

19The protein purification accounts for most of the expenses in recombinant protein production. Hence, the design of a straightforward and cost-effective protein isolation and purification is one of the first steps to be considered in the production strategy.

20There is no single or simple way to purify all kinds of proteins because of their diversity and different properties. Therefore, several strategies have been developed in the past decades to address a broad range of samples. With the introduction of recombinant DNA technology in the seventies, novel affinity tagging methodologies have revolutionized protein purification processes and several easy-to-use affinity tags have emerged since then. Besides the isolation of recombinant proteins, the purification process is also used to concentrate the desired protein. The target protein is usually first designed to be affinity tagged, thus facilitating the purification process and allowing the target protein to maintain its properties without interacting directly with a matrix. However, if the target protein cannot be affinity tagged or if further purification is needed, other purification strategies are added to the process.

21When designing a purification strategy, one must consider the final goal of the target protein to be purified. For instance, recombinant proteins for therapeutic and biomedical applications require a high-level of protein purity and they probably should undergo several subsequent purification steps.

22The available protein purification methodologies separate the target proteins according to differences between the properties of the protein to be purified and properties of the rest of the protein mixture. Recombinant proteins are nowadays purified using column chromatography in scales from micrograms or milligrams in research laboratories to kilograms in industrial settings. The purification of a target protein from a crude cell extract is, however, not always easy and even with all the progresses achieved so far, additional physicochemical-based chromatography methods such as size exclusion (SEC), ion exchange (IEX), and hydrophobic interaction (HIC) are often used to complement the affinity tagging. These methods rely on minor differences between various proteins properties such as size, charge, and hydrophobicity, respectively.

23In a traditional purification pipeline, the chromatography starts with a capturing step, where the target protein binds to the absorbent while the impurities do not. Then, weakly bound proteins are washed out of the column, and conditions are changed so that the target protein is eluted from the column.

24This technique is a non-binding method that separates protein samples with different molecular sizes under mild conditions. Size exclusion chromatography (SEC) can be used for protein purification, in which it usually dilutes the sample, or for group separation, which is mainly used for desalting and buffer exchange of samples. This technique is ideal for the final polishing in a multiple-step purification strategy. Analytical SEC allows the determination of the hydrodynamic radius of protein molecules and the corresponding molecular weight.

25This technique separates proteins with different surface charge and it offers a high-resolution separation combined with high sample loading capacity. The purification relies on a reversible interaction between a charged protein and an oppositely charged chromatography medium. Proteins purified by ion exchange chromatography (IEX) are usually obtained in a concentrated form. The net surface charge of proteins is influenced by the surrounding pH: when the pH is above the protein isoelectric point (pI), the target protein has a negatively charged shield that is used for binding to a positively charged anion exchanger; when the pH is below its pI, the target protein has a positively charged shield that is used for binding to a negatively charged cation exchanger. The IEX purification protocol is initiated under low ionic strength, and the conditions are then changed so that the bound substances can be eluted differentially by increasing salt concentration or changing pH using a gradient or stepwise strategy. In general, the IEX is used to bind the target protein, but it can also be used to bind impurities when required. The IEX is the most common technique used for the capture step in a multiple-step purification strategy, but it can be used in the intermediate step as well.

26Hydrophobic interaction chromatography (HIC) separates proteins according to differences in their surface hydrophobicity by using a reversible interaction between non-polar regions on the surface of these proteins and the immobilized hydrophobic ligands of a HIC medium. The proteins are separated according to differences in the amount of exposed hydrophobic amino acids. This technique is ideal for capture and intermediate steps in a multiple-step purification strategy.

27The interaction between hydrophobic proteins and a HIC medium is influenced significantly by several parameters (reviewed in; ), including:

28(i) The type of the ligand and degree of substitution: the type of immobilized ligand (alkyl or aryl) determines the protein adsorption selectivity of the HIC adsorbent. In general, alkyl ligands show more pure hydrophobic character than aryl ligands. The protein binding capacities of HIC adsorbents increase with increased degree of substitution of immobilized ligand. The degree of substitution is the average number of substituent groups attached per milliliter of gel, and it correlates with the protein binding capacities of HIC adsorbents as follows: higher binding capacities are obtained with an increased degree of substitution of immobilized ligand. At a reasonably high degree of ligand substitution, the apparent binding capacity of the adsorbent remains constant (the plateau is reached) but the strength of the interaction increases. Solutes bound under such circumstances are difficult to elute due to multi-point attachment.

29(ii) The type of base matrix: the matrix should be neutral to avoid ionic interactions between the protein and the matrix, and it should also be hydrophilic. The two most widely used matrices are strongly hydrophilic carbohydrates, such as cross-linked agarose, or synthetic copolymer materials.

30(iii) The type and concentration of salt: a high salt concentration enhances the interaction, while lowering the salt concentration weakens the interaction. The effect of the salt type on protein retention follows the Hofmeister series for the precipitation of proteins from aqueous solutions. In Hofmeister series, the chaotropic salts (magnesium sulfate and magnesium chloride) randomize the structure of the liquid water and thus tend to decrease the strength of hydrophobic interactions. In contrast, the kosmotropic salts (sodium, potassium, or ammonium sulfates) promote hydrophobic interactions and protein precipitation, due to higher “salting-out” or molar surface tension increment effects.

31(iv) pH: when pH is close to a protein’s pI, net charge is zero and hydrophobic interactions are maximum, due to the minimum electrostatic repulsion between the protein molecules allowing them to get closer. In general, an increase in the pH weakens the hydrophobic interaction probably due to an increased titration of charged groups, thereby leading to an increase of protein hydrophilicity. A decrease of the pH may result in an increase of hydrophobic interactions. However, the effect of pH in HIC is not always straightforward.

32(v) Temperature: the role of temperature in HIC is complex, but in general, increased temperatures enhance the protein retention. Careful should be taken when conducting protein purifications at room temperature as the protein performance in the HIC will probably not be reproducible in a cold room, and vice versa.

33(vi) Additives: low concentrations of water-miscible alcohols, detergents, and aqueous solutions of chaotropic (“salting-in”) salts result in a weakening of the protein–ligand interactions in HIC leading to the desorption of the bound solutes. The non-polar parts of alcohols and detergents compete with the bound proteins for the adsorption sites on the HIC media resulting in the displacement of the latter. Chaotropic salts affect the ordered structure of water and/or that of the bound proteins. Both types of additives also decrease the surface tension of water thus weakening the hydrophobic interactions to give a subsequent dissociation of the ligand–solute complex. The use of additives should be carefully considered as they might compromise the target protein structure and activity.

34Proteins bound to HIC media can be eluted using some of the above-mentioned conditions such as reduced salt concentration, increased pH, or addition of alcohols or detergents, but trial-and-error experiments should be conducted to select the best option for each specific target protein.

35Besides protein purification, the HIC methodology offers several potentialities in protein production, being described as one of the most used strategies for endotoxin clearance. It can also be used for protein refolding.

36The HIC methodology has been applied for the purification of calcium-binding proteins (CaBPs;;; ). These proteins expose a large hydrophobic surface in the presence of calcium that can absorb to hydrophobic matrices such as phenyl sepharose, even in the presence of low salt concentration. Most of the contaminant proteins will not bind under these conditions, which benefits the recovery of a pure CaBP. The elution step is often achieved by removal of the bound calcium through the use of chelating agents like EDTA.

37This technique separates proteins through a reversible interaction between the target protein and a specific ligand attached to a chromatographic matrix. The interaction can be performed via an antibody (biospecific interaction), or via an immobilized metal ion (non-biospecific interaction) or dye substance. The affinity chromatography usually offers high selectivity and resolution together with an intermediate-high capacity. The sample is first bound to the ligand using favorable conditions for that binding. Then, the unbound material is washed out of the column and the elution of pure protein is achieved using a competitive ligand or by changing the pH, ionic strength or polarity. This purification strategy can profit from the use of recombinant DNA technology as the affinity tag can be fused to the protein of interest during cloning and it is further presented in the next section.

38Fusion partners or tags are used in E. coli to improve protein production yields, solubility and folding, and to facilitate protein purification. They can also confer specific properties for target proteins characterization and study, such as protein immunodetection, quantification, and structural and interactional studies. Fusion partners can also be of use when producing toxic proteins. An example is the production of antimicrobial peptides (AMPs) by E. coli using cellulose binding modules as fusion partner. The use of carbohydrate-binding modules (CBMs) as fusion partner has also been applied for targeting peptides and/or functionalizing specific supports/biomaterials for biomedical applications. Besides the fusion(s) partner(s) coding gene, E. coli expression vectors can contain a protease recognition sequence between the fusion partner coding gene and the passenger protein coding gene that allows the tag removal when the latter protein is for using in protein therapies, vaccine development and structural analyses.

39Some fusion partners also protect target proteins from degradation by promoting the translocation of the passenger protein to different cellular locations, where less protease content exists. Both maltose-binding protein (MBP) and small ubiquitin related modifier (SUMO) fusion partners present this feature, passing target proteins from the E. coli cytosol for cell membrane and nucleus, respectively.

40When designing a fusion strategy, the choice of the fusion partner depends on several aspects, including:

41(i) Purpose of the fusion: is it for solubility improvement or for affinity purification? Nowadays, a variety of fusion tags that render different purposes are available, and systems containing both solubility and affinity tags like, for instance, the dual hexahistine (His6)-MBP tag, can be designed in order to get a rapid “in one step” protein production. Some protein tags can also function in both affinity and solubility roles, as for instance, the MBP or glutathione-S-transferase (GST; ). If the fusion tag is to be used in protein purification, the cost and buffer conditions are often the criteria for selection. For instance, proteins that require chelating agents as EDTA are not suitable for immobilized metal affinity chromatography (IMAC) via the His6 tag as nickel ions in the affinity matrix are chelated by EDTA.

42(ii) Amino acid composition and size: these two factors should be considered when selecting a fusion partner because target proteins may require larger or smaller tags depending on their application. Larger tags can present a major diversity in the amino acid content, and will impose a metabolic burden in the host cell different from that imposed by small tags.

43(iii) Required production levels: structural studies require higher protein production levels that can be rapidly achieved with a larger fusion tag, which has strong translational initiation signals, whereas the study of physiological interactions demands for lower production levels and small tags.

44(iv) Tag location: fusion partners can promote different effects when located at the N-terminus or C-terminus of the passenger protein. Usually, N-terminal tags are advantageous over C-terminal tags because: (1) they provide a reliable context for efficient translation initiation, in which fusion proteins take advantage of efficient translation initiation sites on the tag; (2) they can be removed leaving none or few additional residues at the native N-terminal sequence of the target protein, since most of endoproteases cleave at or near the C-terminus of their recognition sites.

45Fusion tags can be incorporated using different strategies: affinity and solubility tags are set individually or together, and sites for protease cleavage are designed between the fusion tags and target proteins.

46In spite of all the approaches conducted so far, the choice of a fusion partner is still a trial-and-error experience. Fusion partners do not perform equally with all target proteins, and each target protein can be differentially affected by several fusion tags. In the past decade, parallel high throughput (HTP) screenings using different fusion partners have developed soluble protein production, and facilitated a rapid, tailored, and cost-effective choice of the best fusion partner for each target protein.

47The mechanisms by which fusion tags enhance the solubility of their partner proteins remain unclear, but several hypotheses have been suggested:

48(i) Fusion proteins form micelle-like structures: misfolded or unfolded proteins are sequestered and protected from the solvent and the soluble protein domains face outward;

49(ii) Fusion partners attract chaperones: the fusion tag drives its partner protein into a chaperone-mediated folding pathway. MBP and N-utilization substance (NusA) are two fusion tags that present this mechanism, being previously reported to interact with GroEL in E. coli;

50(iii) Fusion partners have an intrinsic chaperone-like activity: hydrophobic patches of the fusion tag interact with partially folded passenger proteins, preventing their self-aggregation, and promoting their proper folding. MBP was previously reported to act also as a chaperone in the fusion context. Solubility enhancer partners may thus play a passive role in the folding of their target proteins, reducing the chances for protein aggregation;

51(iv) Fusion partners net charges: highly acidic fusion partners were suggested to inhibit protein aggregation by electrostatic repulsion.

52A large variety of solubility enhancer tags are available (Table 1), including the well-known MBP, NusA, thioredoxin (TrxA), GST, and SUMO, and several other novel moieties recently discovered, for instance, the Fh8 tag.

53MBP is a large (43 kDa) periplasmic and highly soluble protein of E. coli that acts as a solubility enhancer tag, and it has a native affinity property to function as a purification handle.

54MBP plays an important role in the translocation of maltose and maltodextrins: it has a natural protein-binding site that it uses to interact with other proteins involved in maltose signaling and chemotaxis, and it has a large hydrophobic cleft close to this site that undergoes conformational changes upon maltose binding.

55When used in the fusion context, MBP promotes target protein solubility by showing chaperone intrinsic activity, and it is more efficient at the N-terminus of the target proteins rather than at the C-terminus. In fact, MBP promotes the proper folding of the target protein by interacting with the latter, and occluding its self-association. This passive role of MBP in protein folding is correlated with the large hydrophobic area exposed on its surface, which is responsible for the contact with other proteins in the maltose transport apparatus. Hence, the MBP hydrophobic cleft is pointed as the site where fused polypeptides interact with the fusion partner, similar to what it is reported for GroEL and DnaK molecular chaperones. The presence of this cleft can explain why only certain soluble proteins like MBP act as solubilizing agents. Moreover, MBP presents certain conformational flexibility associated with the cleft; thereby it can adjust its shape to accommodate several different polypeptides.

56MBP fusion proteins bind to immobilized amylose resins, but this binding is highly dependent on the nature of the passenger protein as it can block or reduce the amylose interaction. Difficulties found in the binding of MBP fusion proteins to amylose resins corroborate the hypothesis that target proteins interact with MBP via its binding site.

57Other affinity tags, specific proteases and protein cultivation strategies are being employed together with MBP to improve protein soluble production, purification and native protein recovery, as for instance, His6-MBP fusions, His6-MBP-TEV fusions, MBP-His6-Smt3 fusions in which the Saccharomyces cerevisiae Smt3 protein is used for protein processing by proteolytic cleavage between the MBP-His6 tags and the protein of interest, and secretion of MBP fusion protein into the culture medium.

58Several commercial expression vectors containing the MBP tag are available for cytoplasmic and periplasmic production of target proteins, including the pMAL series (New England Biolabs) and pIVEX (Roche).

59NusA is a transcription termination/anti-termination protein that promotes/prevents RNA polymerase pausing when acting alone or when included in the anti-termination complex, respectively. NusA (55 kDa) is used as a fusion partner to confer stability and high solubility to its target proteins. The NusA ability to improve the soluble production of fusion proteins may be correlated with its intrinsically solubility and biological activity in E. coli. NusA slows down translation at the transcriptional pauses, offering more time for protein folding. In contrast to MBP, NusA does not present an intrinsic affinity property, therefore requiring the addition of an affinity tag for efficient protein production, as for instance, the His6 tag. As for MBP, several strategies have been exploited to use the NusA solubility enhancer fusion partner with purification tags and specific proteases like the pETM60 vector (EMBL; ) that render the production of a NusA–His6–TEV fusion protein, or the pET43 (Novagen), that offers the same NusA–His6 fusion protein but with a thrombin and enterokinase cleavage sites between the fusion tags and target proteins.

60In spite of the different physiochemical and structural properties, as well as different biological functions, MBP and NusA are often reported to promote similar solubility improvements in their target proteins, being ranked as two of the best tags for making soluble proteins. Both fusion partners were reported to probably work by similar mechanisms, in which NusA, like MBP, plays a passive role on the target protein folding.

61TrxA, or Trx, is a 12-kDa intracellular thermostable protein of E. coli that is highly soluble expressed in its cytoplasm. The E. coli Trx can be used for co-production with a target protein, improving the solubility of the latter. Trx is also commonly employed as a fusion tag to avoid inclusion body’s formation in recombinant protein production by taking advantage of its intrinsic oxido-reductase activity responsible for the reduction of disulfide bonds through thio-disulfide exchange. The fusion partner Trx can be placed both at the N- or C-terminal of target proteins but this fusion partner is more effective at the N-terminal of the target protein. In some HTP screenings, the Trx fusion partner improves target protein solubility similar to MBP tag, being considered one of the best choices for protein production in E. coli.

62Unlike MBP, Trx does not have intrinsic affinity properties, thus requiring an additional fusion tag for protein purification such as the His6 tag. The pET32 (Novagen), one of the commercially available vectors for Trx tagging, carries this dual-fusion partners for protein production and purification.

63Trx fusion partner can also be useful in protein crystallization of certain target proteins because it readily forms several crystals itself, and it offers a rigid connection to the target protein, which is an essential feature for blocking conformational heterogeneity usually found in various attempts of fusion proteins crystallization.

64Small ubiquitin related modifier is a small protein (~11 kDa) found in yeast (one single gene coding for Smt3) and vertebrates (three genes coding for SUMO-1, SUMO-2, and SUMO-3; ) that has recently been used as an effective N-terminal solubility enhancer fusion partner, offering advantages over other fusion systems.

65The robust SUMO protease (catalytic domains of Ulp1) offers significant advantages over other endoproteases because it recognizes the tertiary structure of SUMO, and consequently it does not present unspecific cleavage of the protein linear amino acid sequence. Moreover, when used for tag removal, SUMO protease generates a cleaved target protein with its native N-terminal amino acid composition.

66Small ubiquitin related modifier promotes the proper folding and solubility of its target proteins possibly by exerting chaperoning effects in a similar mechanism to the described for its structural homolog Ubiquitin (Ub; ). Ub was reported to be the nature’s fastest folding protein, and SUMO also presents a tight, rapidly folding soluble structure. In addition, Ub and Ub-like proteins (Ulp) have a highly hydrophobic inner core and a hydrophilic surface that, together with such a rapid folding, may explain the SUMO’s behavior as a nucleation site for the proper folding of target proteins.

67Small ubiquitin related modifier fusion proteins or peptides are usually purified by affinity chromatography using the His6 tag. Due to its unique features, SUMO technology has being constantly explored, and novel strategies for a facile and rapid protein production are now available, as the SUMO–intein system. The SUMO fusion partner is also available for recombinant protein production in other host cells, namely, insect cells and other eukaryotic cells.

68Glutathione-S-transferase from Schistosoma japonicum (26 kDa) that has been used as an affinity fusion partner for the single-step purification of its target proteins. GST can also promote protein soluble production in E. coli, being more efficient when positioned at the N-terminal rather than at the C-terminal end. This fusion partner can protect its target protein from the proteolytic degradation, stabilizing it into the soluble fraction. In spite of performing quite well in some HTP studies, GST is often a poor solubility tag when compared to other commonly fusion partners, rendering the target protein production into inclusion bodies.

69Glutathione transferases are dimeric enzymes that catalyze the nucleophilic addition of the thiol of glutathione to a wide range of hydrophobic electrophilic molecules. Taking this feature into account, GST can be useful for monitoring the protein production and purification via its catalytic activity, and the purification of GST fusion proteins can be easily performed by affinity chromatography using glutathione derivates immobilized into a solid support. GST fusion proteins can be eluted with glutathione under mild conditions.

70A major disadvantage for using GST as solubility and affinity tag relies on its oligomerized form: GST has four solvent exposed cysteines that can provide a significant oxidative aggregation, making it a poor choice for tagging oligomeric target proteins.

71As occurs with MBP, GST can be coupled with other affinity strategies, for instance, the His6 tag, to improve the protein purification. GST expression vectors like the pGEX or pCold-GST usually contain a protease recognition site between the fusion tag coding gene and the target protein coding gene for GST tag’s removal after or during protein purification.

72GST has also been applied as a fusion partner in other expression systems apart from the E. coli such as yeast, insect cells, and mammalian cells. This fusion partner has shown to be useful for protein labeling, antibody production, and vaccine development.

73In addition to these commonly used fusion partners, new solubility enhancer tags are constantly emerging in literature (see the corresponding references in Table 1), as for instance, the Fh8 tag [see The Novel Fh8 Fusion System (Hitag®)], HaloTag, which uses a modified haloalkane dehalogenase protein that improves protein solubility and can bind to several synthetic ligands, the monomeric mutant of Orc protein of the bacteriophage T7 (Mocr), the E. coli protein Skp, stress-responsive proteins RpoA, SlyD, Tsf, RpoS, part of the domain I of IF2 (expressivity tag), the E. coli secreted protein A (EspA), and the SNUT tag, which is a protein derived from a portion of the bacterial transpeptidase sortase A of Staphylococcus aureus.

74Affinity fusion partners have widely contributed for the development of recombinant protein production studies in basic research and in HTP structural biology by simplifying protein purification procedures, and allowing for protein detection, and characterization.

75Affinity purification handles can be divided into two groups: (1) peptides or proteins that bind a small ligand immobilized on a solid support, as for instance, the His6 tag and nickel affinity resins, and (2) tags that bind to an immobilized molecule such as antibodies.

76The purification of a target protein using an affinity handle offers several advantages over the conventional chromatographic methodologies, namely:

77(i) The target protein never interacts directly with the chromatographic resin;

78(ii) Target proteins can be easily obtained pure after a single-step purification;

79(iii) Affinity purification offers a variety of strategies to bind the target protein on an affinity matrix;

80(iv) Affinity tags are an economically favorable and time-saving strategy, and they allow different proteins to be purified using a common method in contrast to highly customized procedures used in conventional chromatographic purification.

81An affinity tag is often chosen taking into account the purification costs: different affinity media and elution principles present different expenses during the operation process and should therefore be carefully selected at the beginning of the cloning strategy. The buffer requirements are also essential for the designing of an efficient purification strategy. In addition, the choice of an affinity can also rely on the size: small tags are useful for protein detection and antibody production, as they are not immunogenic as large tags.

82Tandem affinity purification (TAP) or dual-tagging strategies are now commonly used in recombinant protein production: they offer a highly specific isolation of target proteins with minimal background and under mild conditions, and they are very useful in the study of protein interactions, allowing the separation of different mixed protein complexes.

83Table 2 lists some of the common and novel purification tags used in recombinant protein production.

84The polyhistidine affinity tag or His tag consists of a variable number of consecutive histidine residues (usually six) that coordinate, via the histidine imidazole ring, transition metal ions such as Ni2+ or Co2+ immobilized on beads or a resin for IMAC. Commonly used IMAC resins such as nitrilotriacetic acid agarose (Ni–NTA, from Qiagen), or carboxymethylasparte agarose (Talon, from ClonTech) have a high binding capacity, and can be used for purification of fusion proteins directly from crude cell lysates.

85The His tag is one of the most widely used purification tags, and it offers several advantages:

86(i) Its small size and charge rarely interferes with protein function and structure;

87(ii) It can be used under native and denaturing conditions

88(iii) Target proteins can be eluted under mild conditions by imidazole competition or low pH.

89The His tag has been used in several HTP screenings, placed at the N- or C-terminal end, or even in the middle of the fusion protein, and it is also an useful tool in protein crystallization as well as protein detection.

90Taking into account the mechanism of protein interaction with the immobilized ions, careful should be taken in IMAC to avoid strong reducing and chelating agents in any of the buffers (as for instance, EDTA), as they will reduce or strip the immobilized metal ions.

91Epitope tags are short sequences of amino acids that serve as the antigen region to which the antibody binds, being suitable for several immunoapplications. These include affinity chromatography on immobilized monoclonal antibodies, and protein trafficking in vitro or in cell cultures. Epitope tagging engages an expensive purification that often limits its wide application.

92The following partners are often used as epitope tags: the FLAG tag, the hemaglutinin, and the c-Myc. Their short sequences rarely interfere with structure or function of target proteins, and are very specific for their respective primary antibodies. The FLAG tag is a short hydrophilic eight amino-acid peptide, and it was the first tag to be used in the epitope context. This tag works either for protein detection or purification, and it has an intrinsic enterokinase cleavage site at its C-terminus end, allowing its complete removal from the target protein.

93Strep II tag is a short tag of only eight amino acid residues that possesses a strong and specific binding to streptavidin via its biotin pocket. This affinity partner can be fused at both N- or C-terminal ends, or within the target protein. Strep II-fused proteins elute from streptavidin columns with biotin derivates under gentle conditions.

94The CBP tag is a calmodulin-binding peptide derived from the C-terminus of skeletal muscle myosin light chain kinase, and it has been used as an N- or C-terminal affinity tag of target protein purification on a calmodulin immobilized matrix. The CBP interaction with calmodulin is calcium-dependent, and hence, the addition of calcium-chelating allows the single step elution of target proteins under gentle conditions. This tag is an affinity system highly specific for protein purification in E. coli but not in eukaryotic systems, as E. coli does not contain endogenous proteins that interact with calmodulin.

95In addition to the above-mentioned affinity tags, new affinity purification strategies are now described in literature for protein isolation and detection (see the corresponding references in Table 2) such as the Fh8 tag [see The Novel Fh8 Fusion System (Hitag®)], cellulose-binding domains I, II, and III (CBD), the HaloTag, the dockerin domain Dock tag, and the avidin-like protein, Tamavidin tag.

96The removal of the fusion partner from the final protein is often necessary because the tag can potentially interfere with the proper structure and functioning of the target protein.

97Fusion partners are removed from their target proteins either by enzymatic cleavage, in which site specific proteases are used under mild conditions, or by chemical cleavage, like for instance formic acid, that offers a less expensive tag removal but it is also less specific compared to the enzymatic strategy, besides presenting harsh conditions that can affect the target protein stability and solubility. Fusion partners can also be cleaved from the target protein using an in vivo cleavage strategy, in which a controlled intracellular processing (CIP) is applied as follows: the fusion protein and protease are produced from separate compatible expression vectors that can be regulated independently of one another. The protease cleaves the fusion protein in vivo, offering the advantage of not compromising the target protein’s purity level or its production yields like often occurs in in vitro cleavage strategies.

98The efficiency of the enzymatic removal of fusion proteins may vary in an unpredicted manner with different proteins, and it often requires the optimization of cleavage conditions through a trial-and-error process. Two types of proteases can be used for tag removal (reviewed in ):

99(i) Endoproteases: they are divided into serine proteases such as the activated blood coagulation factor X (factor Xa), enterokinase, and α-thrombin, and viral proteases like the tobacco etch virus (TEV), and the human rhinovirus 3C protease (Table 3). In spite of recognizing a similar number of substrate amino acid residues, viral proteases have usually more stringent sequence specificity than serine proteases, presenting also slower rates than the latter. Endoproteases are useful tools for the removal of N-terminal fusion tags, since they cleave close to the C-terminus end of their recognition sites thus leaving the target protein with its native N-terminal sequence.

100(ii) Exoproteases: they are often used together with endoproteases mainly for the removal of C-terminal fusion tags. The available exoproteases include metallocarboxypeptidases, and aminopeptidases.

101The removal of a fusion tag is usually accomplished by two purification steps, as follows: after the initial affinity purification step (e.g., via a histidine tag located at the N-terminal of the fusion protein), the purified fusion protein is mixed in solution with the endoprotease (e.g., a his-tagged protease) to cleave off the tag. The cleaved target protein is recovered in the flow-through sample after a second affinity purification step, in which the cleaved fusion tag and the added protease are collected in the eluted sample.

102In spite of widely employed, the removal of fusion partners has always been the Achilles’ heel of affinity tagging, presenting several difficulties such as:

103(i) Unspecific cleavage due to the recognition of a linear amino acid sequence (except for SUMO protease);

104(ii) Inefficient processing due to steric hindrance or the presence of unfavorable residues around the cleavage site. The inclusion of extra amino acid residues (a spacer or linker) between the cleavage site and target protein can alleviate this problem;

105(iii) Low protein yields after tag removal, and failure in recover active, structurally organized target proteins due to protein precipitation and aggregation;

106(iv) High costs of proteases and tedious optimization of cleavage conditions.

107Independently of the cleavage type, additional chromatographic steps are often required to purify the target protein from the cleavage mixture. Although conventional affinity technologies have greatly simplified recombinant protein production, resins, and buffers are still too expensive. Hence, the tag removal adds another layer of complexity and expense to the recombinant protein production process.

108Self-cleaving tags are a special group of fusion tags that possess inducible proteolytic activity, therefore being considered an attractive alternative to the existent affinity strategies for simple and costless protein purification and tag removal.

109The protein splicing is a process in which the intervening sequence (intein) removes itself and binds the flaking residues (exteins) to produce two independent protein products. Self-cleaving tags undergo specific cleavage upon being triggered by low molecular weight compounds or upon a change of conformation. The available technologies include inteins, the S. aureus sortase A, the N-terminal protease (Npro), the Neisseria meningitides iron-regulated protein FrpC, and the cysteine protease domain secreted by Vibrio cholerae, all of them reviewed in.

110Fh8 (GenBank ID: AF213970.1) is one of the promising new fusion technologies, advancing the existing tags by acting simultaneously as an effective solubility enhancer partner and robust purification handle. Actually, the Fh8 is one of the few existent fusion tags to offer this combined feature of enhancing protein solubility and purification, and its low molecular weight (8 kDa) is also a great advantage over other large fusion partners for recombinant protein production in E. coli.

111The Fh8 is a small antigen (8 kDa) excreted-secreted by the parasite F. hepatica in the early stages of infection. This protein is located on the surface of the parasite, and it was suggested as a useful tool for the diagnosis, vaccine, and drug development against F. hepatica infections. The use of recombinant Fh8 produced in E. coli led to the development of a novel, rapid, and simple immunodetection of F. hepatica infections. Moreover, when produced recombinantly in E. coli, the Fh8 revealed to be a highly soluble and unusual thermal stable protein (keeping secondary structure integrity up to 74°C;; ).

112The Fh8 has high homology with 8-kDa calcium-binding proteins (CaBPs) of Schistosoma mansoni (Sm8; ), of Clonorchis sinensis (Ch8), and of S. japonicum (Sj8; ), and it belongs to the calmodulin-like EF-hand CaBP family.

113CaBPs are structurally organized by EF-hand motifs, which are helix–loop–helix structures that participate in Ca2+ coordination. Upon calcium binding, Ca2+sensor proteins, like calmodulin and troponin C, translate the physiological changes in calcium levels by undergoing a conformational change. This then allows the binding of other proteins downstream the process. In EF-hand proteins, the open of the EF-hand structure exposes a hydrophobic surface, which binds the target sequence. Ca2+ buffer proteins, such as calbindin D9k and parvalbumin, are involved in calcium signal modulation, undergoing minimal conformational changes upon calcium binding.

114The Fh8 presents two EF-hand motifs, and it was characterized as a Ca2+sensor protein: when calcium binds, the Fh8 switches from a closed (apo-state) to an open (calcium-loaded state) conformation due to the reorientation of the four helices, exposing a large hydrophobic region that acts as a target-binding surface.

115Previous studies for the prediction of the Fh8 three-dimensional structure (unpublished data) showed that almost all the Fh8’s amino acid sequence is involved or affected by the calcium-binding, with the exception of small residue sequences in the N-terminal (11 amino acid residues) and C-terminal (six amino acid residues). Considering that the N-terminal of a protein is very important for its half-life, the first N-terminal 11 residues of Fh8 were named the “H sequence” and were initially suggested to play a key role in the stability and production of the entire Fh8 protein. This H sequence could also be critical for the immunological response of the Fh8 antigen.

116Taking into account the Fh8 high solubility and stability when expressed in E. coli together with its calcium-binding properties, and given the potential importance of the H sequence, both Fh8 and H peptides were suggested to function as fusion tags for protein production and solubility in E. coli, protein purification, and antibody production.

117The application of both Fh8 (8 kDa) and H (1 kDa) peptides as fusion tags for protein overproduction in E. coli was first reported by Conceição and co-workers, using the following recombinant proteins: a 12-kDa surface protein of Cryptosporidium parvum (CP12), the interleukin-5 of human origin (IL-5), and an oocyst wall protein of Toxoplasma gondii (TgOWP; ). This initial study showed that both Fh8 and H peptides have indeed a positive effect on the E. coli production levels of all target proteins, reaching values three- to 16-fold higher than those obtained with non-fused target proteins.

118The Fh8 and H fusion tags were then studied as solubility enhancer tags, and their performance was compared with other commonly used fusion tags available in the Protein Expression and Purification Core Facility of the European Molecular Biology Laboratory. Figure 2 illustrates the schematic pathway from protein production to purification with the studied solubility tags (His6 tag, GST, MBP, NusA, Trx, SUMO, H, and Fh8). Here, the selected target proteins included the 12-kDa surface protein of C. parvum (CP12), the lectin frutalin from the Artocarpus incisa plant (FTL;,,, ), and four proteins from the yeast S. cerevisiae: reduced viability upon starvation protein 167 (RVS167), phospholipase D1 (SPO14), and serine/threonine-protein kinases 1 and 2 (YPK1 and YPK2). These target proteins were all known as difficult-to-express in E. coli, and presented different molecular weights, locations, and functions. The evaluation of their solubility and consequent effect of each fusion tag was performed after nickel affinity purification and upon tag removal in 10-mL cultures and in 500-mL cultures.

119This comparison study showed that the Fh8 fusion partner stands among the well-described best fusion partners, MBP, NusA, and Trx, for soluble protein production. For the proteins tested, both GST and H fusion tags did not improve target protein solubility in E. coli.

120The novel Fh8 fusion partner is thus an excellent candidate for testing production and solubility next to the other well-known fusion tags. Its low molecular weight and its solubility enhancing effect make Fh8 an advantageous option compared to larger fusion tags for soluble protein production in E. coli.

121Apart from its solubility enhancer effect, the Fh8 was also explored by, as a purification handle via its calcium-binding behavior combined with HIC. Two different model proteins were used within this study: green fluorescent protein (GFP) and superoxide dismutase (SOD), and the Fh8-HIC performance was also compared to the one of His tag technology (via IMAC).

122Figure 3 resumes the purification mechanism of target proteins using the Fh8-HIC strategy. As previously mentioned, the Fh8 is a Ca2+-sensor protein that opens its structure upon calcium accommodation. The opening of the Fh8’s structure exposes a large hydrophobic surface that becomes available for interaction with its targets. In this study, the Fh8 tag and Fh8-fused proteins presented a calcium-dependent interaction with a hydrophobic resin, and, as reported for other calcium-binding proteins, this interaction was still occurring even with low salt concentration in the mobile phase. The low salt concentration decreases the unspecific binding of other proteins from the E. coli extracts, thus promoting selectivity toward the purification of the fusion protein of interest. Moreover, it was also shown that, as a calcium-binding protein, the Fh8 tag and Fh8-fused proteins can be eluted by using a calcium chelating agent, such as EDTA. One can also use for elution a mobile phase with an increased pH (e.g., pH 10), which creates a net charge that destabilizes hydrophobic interactions. This elution strategy allows a single-step and rapid elution of all bound proteins.

123The Fh8-HIC methodology presented also the advantage of being compatible with the IMAC technique, thus, allowing a dual protein purification strategy that can be used sequentially, complementing each other, to obtain an active and more purified protein when desired. In addition, the use of two consecutive purification steps and the distinct nature of HIC and IMAC methodologies is known to help for the efficient removal of contaminating proteins.

124Regarding the H tag, it did not function as a solubility enhancer tag, but it improved the production levels of target proteins in E. coli similarly to the Fh8 tag. Taking that into account, the H tag was further explored for the recombinant production of antigens of interest in E. coli, and their subsequent immunization and polyclonal antibody production.

125The major novelty of the H tag relies on its small size (1 kDa) combined with the adjuvant-free immunization of antigens. Figure 4 shows the schematic pathway of using the H fusion tag from gene to antibody.

126showed a successful case study with the CP12 antigen, which has a low molecular weight that can hinder the production of polyclonal antibodies. The HCP12 fusion antigen elicited an earlier immune response and higher (approximately 2-fold) polyclonal antibody titers than the non-fused CP12. This application study demonstrated that the H partner improves the specific polyclonal antibody production against the CP12 antigen without using adjuvants, and the resulting polyclonal antibodies can be used as a diagnostic tool for immunodetection of C. parvum infections in humans or animals.

127Apart from CP12, several H-fused antigens have already been produced in E. coli and immunized in mice and rabbits, such as, the human interleukin-5 (IL-5), the cyst wall protein-1 from T. gondii (TgOWP), the cyst wall protein from Giardia lamblia cysts (CWG), the β-giardin cytoskeletal protein of the ventral disk from the G. lamblia trophozoite (βG), the cyst wall specific-glycoprotein Jacob from Entamoeba histolytica (Ent), and the falcipain-1 trophozoite cysteine proteinase from Plasmodium falciparum (Pfsp), among others.

128The growing demand for effective health and environmental biotechnology resources has advancing the design of different strategies for the successful protein production in E. coli. Its benefits of cost and ease of use and scale make E. coli one of the most widely used host systems for recombinant protein production, but one must be aware that success is not always guaranteed in this prokaryotic host system, mainly when working with recombinant proteins of human origin.

129This review highlighted several key factors that contribute to the soluble protein production and purification in E. coli, including the use of different mutated host strains, co-production of chaperones and foldases and testing different cultivation conditions, with a main focus in the gene fusion technology.

130The use of fusion partners was an important turning point for the E. coli host system: fusion tags promote or increase protein solubility, help on protein purification and can also be used to increase protein’s immunogenicity. Traditional fusion systems like MBP, GST, NusA, or Trx have constantly been challenged and complemented by novel fusion solutions such as the SUMO tag, the HaloTag, the SNUT tag, and the expressivity tag, among others.

131More recently, a novel and unique fusion system for simple and inexpensive soluble protein overproduction and purification in E. coli was developed and studied: the Fh8 tag.

132The Fh8 is ranked among the best solubility enhancer tags as Trx, MBP, or NusA, and it offers a specific and simple purification of the target proteins by using its natural calcium-binding properties and mild conditions for HIC. The Fh8 fusion partner is one of the few existing tags to promote simultaneously target protein solubility directly into the E. coli cytoplasm and a simple and cost-effective protein purification.

133The novel Fh8 fusion system overcomes several issues related with recombinant protein production in E. coli: by using a straightforward methodology, this novel system increases protein production levels, promotes protein solubility and low cost purification, and helps for protein immunogenicity, in which the H tag facilitates a simple, rapid, and adjuvant-free production from gene to antibody. This novel fusion system offers the great advantage of combining these four abilities into the two lowest molecular weight fusion partners described so far. Hence, the Fh8 fusion system appears as a valuable tool for the efficient and economical recombinant protein production in E. coli.

134While this review applies to the use of Fh8 and H tags for recombinant protein production in bacterial host systems, it is hoped that the novel fusion system presented here will apply to other hosts, as for instance, eukaryotes and mammalian cells and thus, this must be investigated.

135Despite being widely employed to improve soluble protein production in E. coli, fusion tags are not yet well comprehended as suggested by the general lack in literature of studies regarding their mechanism of action. Therefore, efforts should be taken to disclose how fusion tags work while promoting such a positive effect in the protein production in E. coli. Perhaps, a wide systems biology analysis can help to reveal the different pathways that fusion tags undergo in E. coli, leading also to their organization into functional groups.

136Taking into account the broad range of applications, the trend is that the number of available fusion tags will increase, and the understanding of their way of action will, undoubtedly, allow the development of tailored-made tools for protein production.

137Sofia Costa drafted the review, participated in the study design of the novel Fh8 and H fusion tags, and in most of its experimental work. André Almeida, António Castro, and Lucília Domingues participated in the study design of the novel Fh8 and fusion tags. Lucília Domingues conceived and helped to draft the review. All authors read and approved the final manuscript.

138The Fh8 tag utilization for the improvement of protein production in E. coli and the Htag utilization for the production of immunogens and corresponding polyclonal antibodies are covered by worldwide patents (WO 2010082097 and WO 2011071404, respectively), both licensed to Hitag Biotechnology, Lda. The authors Sofia Costa, André Almeida, and António Castro are co-owners of the patent and are associated with Hitag Biotechnology, Lda.