3.1. Galectin purification on glycoprotein columns
Apart from the recombinant production of galectins, the isolation of recombinant-produced galectins from the crude extract is a crucial step for implementing
in-vitro binding studies. Our studies used a two-step purification step consisting of two successive affinity purifications, including IMAC and glycoprotein affinity resin. IMAC is a well-established, commercially available purification system often used to isolate recombinant galectins [
28]. We captured mg amounts of galectins from the bacterial crude extract, which is in good accordance with previous results [
15,
22,
23,
50]. Since IMAC takes advantage of the strong affinity of metal ions to histidine-peptides but does not separate active from non-active galectins, we considered using IMAC as a preselected step to get rid of the central part of the bacterial host proteome. In former studies, we used commercially available lactose-agarose resins as the second chromatography step to purify Gal-3 and Gal-3 fusion proteins [
22,
23]. Here, pressure issues probably caused by the agarose resin hampered sample application and general handling. Apart from this, the affinity of galectins towards lactose is weak [
51], and we could not purify all galectins from our library with this ligand. Furthermore, the Glucose moiety from lactose is presented in open ring conformation due to the coupling chemistry to the crosslinked agarose and may also disturb the galectins’ binding. In the past years, the multivalent presentation of ligands became crucial for increasing the galectin affinities to glycan ligands [
14,
15,
50]. Since ASF and fetuin were identified as suitable multivalent binders for galectins [
19,
44], we established glycoprotein-decorated affinity resins based on these natural multivalent glycoproteins. We coupled ASF and fetuin to CNBr-activated Sepharose
TM 4 Fast Flow with 15 mg/mL ± 0.7 mg/mL for asialofetuin and 16.4 mg/mL ± 0.9 mg/mL for fetuin, respectively (
Table S1). These coupling results match the manufacturers’ information related to the coupling of α-chymotrypsinogen to CNBr-activated Sepharose (Affinity Chromatography Handbook Vol. 3: Specific Groups of Biomolecules, Cytiva). Apart from
N-hydroxysuccinimide (NHS)- or epoxy-activated Sepharose resins, the CNBr-activated Sepharose represents a suitable pre-activated chromatography medium to couple glycoproteins by lysine residues of the protein side chains [
52].
We characterized our galectin libraries’ binding properties with these glycoprotein resins, including His
6-tagged and fusion proteins of Gal-1C2S, Gal-3, Gal-8N, and Gal-8C. Our results revealed that ASF was the best binder for HGal-1C2S with almost 70 % eluted (
Figure 1A), followed by HGal-3 with 30 %. ASF is the desialylated form of the natural multivalent glycoprotein fetuin consisting of three tri-antennary galactose-presenting glycans and five to six core-1 O-glycan structures [
53]. The binding of both galectins to ASF or
N-acetyllactosamine (LacNAc)-terminated oligosaccharides is consistent with previous studies [
44,
54,
55]. We also found that 25 % of HGal-8N was bound to the column, although it prefers sialylated epitopes over galactosyl-terminated oligosaccharides. In contrast, we found the lowest binding for HGal-8C (3 %), which has a higher affinity towards non-sialylated structures [
56,
57].
We further characterized the binding of the His
6-tagged galectins on the fetuin-decorated resin (
Figure 1B). Here, we observed that fetuin is a binder for HGal-8N (66 %) which is due to the terminal sialylation of fetuin [
53]. The N-glycans of fetuin are composed of two terminal α2,3–linked and one α2,6-linked sialic acid residue. The O-glycan is α2,6-sialylated at the
N-acetylgalactosamine (GalNAc) and α2,3-sialylated at the galactose moiety. The preference of the Gal-8 N-terminal domain for sialic acid residues, especially for α2,3 residues, was already described in previous studies [
56,
57]. In contrast, we detected no binding of the Gal-8C-terminal domain on the fetuin-resin, which reflects previous studies that Gal-8C binds preferentially non-sialylated oligosaccharides such as (poly)-LacNAc and blood group antigens [
56,
57,
58,
59,
60]. We additionally detected binding of Gal-1 and Gal-3 with 30 % and 48 %, respectively. In former studies, it was found that both galectins bind α2,3 sialylated LacNAc epitopes [
55]. Furthermore, sialic acids may have been lost through the coupling process to Sepharose, which could have contributed to the binding of HGal-1 and HGal-3. However, the maintenance of the sialic acids under coupling conditions was confirmed (
Figure S1). The lack of HGal-8C binding to sialylated epitopes follows previous studies [
51,
56,
57,
58,
59,
60].
For the His
6-SNAP-fluorescent protein-galectin fusion proteins, we observed lower binding to the ASF (
Figure 1A) and fetuin (
Figure 1B) affinity resins. HSYGal-3 bound best equally to ASF (12 %) and fetuin (11 %), whereas higher binding of HSeGFPGal-8N (25 % binding) to fetuin was observed as seen for HGal-8N. No binding was found for HSeGFPGal-8C on both affinity resins. The fusion protein HSDsRedMGal-1C2S bound only to the ASF-resin in contrast to HGal-1C2S. An exception was the fusion protein of Gal-8N with 25 % binding. We conclude that only a fraction of IMAC-purified galectin fusion proteins can bind to the affinity resins and are expressed as active-binding galectins. However, the well-known binding properties of the galectins are similarly reflected for the galectin fusion proteins.
We analyzed the collected IMAC fractions for all galectins by SDS-PAGE (
Figure 2, S6, S8, S10). Fractions of solely His
6-tagged galectins mainly displayed the mass corresponding to the molecular weight of these galectins with small impurities. Apart from this, the IMAC fractions of the galectin fusion proteins exhibited the mass of the whole fusion protein and several additional smaller bands with lower molecular weights, probably resulting from protein fragmentation.
We conclude that this fragmentation leads to lower yields in the glycoprotein resin chromatography for the galectin fusion proteins. In addition, yield fluctuations due to different galectin expression batches may also contribute to the overall yield of galectin gained after purification with glycoprotein resin (
Figure S3). On the example of the fusion protein HSYGal-3, we examined the fragmentation which was visible in the IMAC eluate in more detail (
Figure 2). The band at 74 kDa corresponds to the molecular size of the complete fusion protein HSYGal-3 (
Figure 2C). Fragments that appeared at 55 kDa and 20 kDa correspond to the mass of His
6-SNAP and YFP-Gal-3. It may arise from enterokinase cleavage, as described previously [
22]. The bands at 24 kDa and 28 kDa can be assigned to the mass of YFP and Gal-3, respectively. Protein sequence analysis of the fusion protein regarding proteolytic cleavage pointed to a trypsin cleavage site between the last tyrosine residue of eYFP and the starting methionine residue of the Gal-3 protein (results not shown). However, the use of proteolytic inhibitors should prevent the observed fragmentation. Considering the fusion of four protein subunits, the fragmentation could be further induced by the IMAC procedure or result from translation abortion in protein translation. We further excluded that the fragmentation is caused by the storage conditions such as storage temperature and time (
Figure S7).
We analyzed the purity of the His
6-tagged galectins and galectin fusion proteins after ASF and fetuin affinity purification by SDS-PAGE (
Figure 2, S8, and S10). The purity was increased for all galectins eluted after glycoprotein affinity chromatography, indicating the purification process’s functionality. In the case of HGal-3 and HSYGal-3, protein fragments of different sizes first detected in the IMAC eluate appeared in the flow-through and wash fractions (
Figure 2) since only active galectin-CRDs can bind to the ASF-decorated resin. For HSYGal-3, we observed two single bands in the ASF eluate with calculated molecular sizes of approximately 70 kDa and 28 kDa (
Figure 2C, lane 4). These bands were also detected in the Western blot by an anti-Gal-3-antibody (
Figure 2D, lane 4). Accordingly, the two bands can be assigned to the complete fusion protein HSYGal-3 and the single CRD domain of Gal-3, respectively. As described above, we assume that the Gal-3 domain was cleaved off from the complete fusion protein after IMAC purification and was subsequently purified by binding to the ASF-resin.
The increase in purity for HSYGal-3, HYGal-3, HSGal-3, and HGal-3 was additionally proven by SEC (
Table 1 and
Figure S11). Especially in the IMAC fractions of HSYGal-3 and HSGal-3, molecular masses corresponding to His-SNAP fragments were detected and strengthened the assumption of fusion protein cleavage between the SNAP-tag and the eYFP fluorescent protein. Furthermore, we observed a protein fraction in the washing step for some of the galectins in both the ASF-Sepharose (His
6-tagged and fusion protein of Gal-8N and Gal-1C2S) and Fetuin-Sepharose purification (HSYGal-3 and HGal-8N) (
Figure S8 A-D and
Figure S10B 5a-12d). The appearance of the galectin in the wash step can probably be traced back to misfolded and inactive galectin. As we have purified several galectins with one column, the age of the column material may also contribute to the loss of active galectin in the eluate fraction. Generally, the galectin fusion proteins’ molecular weight is higher than the His
6-tagged galectins. Therefore, the fusion proteins occupy a larger space, and thus other galectins could be prevented from accessing the glycans of the ASF. For Gal-8C proteins, we have observed meager yields during glycoprotein affinity purification (
Figure 1), which we have traced back to the absence of a suitable glycan ligand, as described above. The SDS-PAGE analysis of IMAC fractions demonstrated recombinant expression of HSeGFPGal-8C (
Figure S8F) and underlines our result that ASF and fetuin are unsuitable for affinity purification. The evaluation of the binding behavior of HGal-8C to the columns was hampered by a weak protein expression whose presence could only be detected by Western blot (
Figure S8E and
Figure S9).
After two-step purification, we obtained low amounts of galectin, as we only applied 0.2 µmol galectin on the column to characterize the binding to the glycoproteins. Furthermore, we used only 1 mL of Sepharose-medium for purification. Higher volumes of chromatography media, for example, 5 mL instead of 1 mL, may allow the application of the whole IMAC eluate and could contribute to increased amounts of eluted protein after two-step purification.
Galectins are mainly purified in a one-step process by adding functional tags such as His
6-tags or GST-tags [
24,
27,
28,
29]. The co-purification of inactive galectins due to misfolding or translational issues is not excluded. The direct one-step isolation of galectins with ASF matrices was also used in other studies for the affinity purification of Gal-3 [
45,
46]. Here, the maintenance of the column material could be impaired by glycosidases or proteases of the crude extract, which emphasizes the importance of a preceding purification step. In our study, introducing the second chromatography step enabled an efficient separation of protein fragments, especially in the case of galectin fusion proteins.
In contrast to our approach, a combination of DEAE-Sepharose and ASF-Sepharose was applied to purify Gal-1 from the bovine spleen with 58% recovery [
33]. However, we could not cover the glycan binding specificities of all tested galectins with ASF and fetuin. The application of multivalent tailor-made glycans, such as neo-glycoproteins, shall enable the specific fine purification of these galectins [
14,
15,
50,
61]. Defined glycans were also used for fine purification [
36]. Here, the purification of mouse Gal-1 mutants with a Galβ1-4Fuc-decorated resin was more efficient than an ASF resin. In addition, the CaRe method is a suitable alternative for the isolation of Gal-3. This procedure provides the isolation of Gal-3 by specific multivalent capturing agents without the use of solid chromatography resins [
30,
31,
32]. Here, recombinant Gal-3 was purified from the crude extract with high purity using chondroitin sulfate A and C or bovine thyroglobulin as capturing agents and β-lactose as releasing disaccharide.
3.2. Binding of galectins to ASF and ECM glycoproteins
We investigated the binding properties of His
6-tagged Gal-3 and Gal-3 fusion proteins in solid-phase assays with ASF-coated microtiter plates. For HGal-3, the fractions of IMAC and IMAC/ASF chromatography showed similar apparent
KD values and binding efficiencies (
Table 2). The apparent
KD values are in good accordance with former results for HGal-3 [
23]. The consistency before and after the fine purification can be traced back to the high purity of the protein after IMAC (
Figure 2A, lane 4).
Compared to HGal-3, we observed lower apparent
KD values for all SNAP-tag harboring Gal-3 fusion proteins (
Table 2). For HSYGal-3, for example, this is due to a higher binding signal and lower standard deviations after ASF chromatography compared to IMAC-purified HSYGal-3 (
Figure 3). However, by applying the second purification step, we expected a similar binding behavior of HSYGal-3 to that of HGal-3 due to the removal of the fragments that occurred after IMAC. We conclude that the apparent higher affinity of the galectin fusion proteins is independent of the purification mode and may be attributed to the fusion partners.
We then focused on the binding properties of different fusion protein versions of Gal-3 in the same binding assay to evaluate the influence of the single fusion partners SNAP-tag and fluorescent protein eYFP. Comparing the binding properties of solely IMAC-purified fusion protein HSYGal-3, HSGal-3, and HYGal-3 with HSY as control revealed the highest binding signal for the SNAP-tagged proteins HSGal-3 followed by HSYGal-3 (
Figure S14). The use of IMAC and glycoprotein affinity purified fusion proteins did not affect the binding behavior of HSGal-3 but led to an increase of the binding signal for HSYGal-3 and resulted in a similar binding signal of HSGal-3 (
Figure 4). We conclude those fusion proteins that involve more than three partners, like HSYGal-3 are susceptible to fragmentation which leads to apparent changes in binding behavior. On the other hand, the necessity for double purification of galectin fusion proteins is demonstrated. However, despite using double-purified fusion proteins of Gal-3, we still observed higher binding signals for SNAP-tagged galectins in contrast to HYGal-3, which we have also observed in a previous study [
23]. As we use antibody-based His
6-tag detection by default, we excluded a methodology-based issue causing this effect by detecting the galectin binding through fluorescence (
Figure S15). The fluorescent protein eYFP tends to form weak dimers at high concentrations [
62,
63]. Therefore, the contribution of eYFP to the appearance of a higher binding signal cannot be entirely excluded. Stöhr et al. reported an increase in fluorescence intensity of fluorescent proteins upon labeling with SNAP-tag [
64], which could explain the enhanced binding signal of HSYGal-3 compared to HYGal-3 observed in the fluorescence detected assay (
Figure S15). As we additionally observed a higher binding signal and lower apparent
KD value for the fusion protein without fluorescent proteins (HSGal-3) (
Figure 4,
Table 2), we conclude that the SNAP-tag induces oligomerization of the galectin fusion proteins resulting in higher binding signals and an apparent higher affinity. To the best of our knowledge, the oligomerization ability of the SNAP-tag is not reported in the literature. The SNAP technology is based on the DNA repair protein
O6-alkylguanine-DNA transferase (hAGT), which irreversibly transfers an alkynyl group to its cysteine group from
O6-alkylguanine-DNA [
65]. The crystal structure of the human monomeric SNAP-protein (RCSB PDB entry: 3KZY) displays a tertiary structure consisting of three sheets in an antiparallel direction and eight helical structures. Parts of the sheet, loop, and helical areas of the SNAP-protein consist of amino acid side chains with positive hydropathic score values (aa 30-41 from third sense sheet; aa 44-61 from loop region; aa 104-150 of the helical area) which indicate hydrophobic regions [
66]. Therefore, it might be possible that the SNAP proteins interact via hydrophobic interactions under given conditions. SEC measurements of the control fusion protein HSY demonstrated the dimeric form of the protein (
Figure S12), which underlines a possible contribution of the SNAP-protein and the fluorescent protein eYFP. However, SEC measurements of the double-purified fusion proteins only displayed the monomeric form of the galectin-3 protein and did not support our assumption (
Table 1 and
Figure S11). The absence of oligomeric structures is probably due to the measuring conditions during the SEC run. Here, protein dilution occurs as the sample flows through the column, which probably prevents the concentration-dependent formation of oligomers. In contrast, the galectins are concentrated in a smaller volume in the microtiter plate in the presence of a multivalent ligand such as ASF.
Binding assays with fusion protein versions of Gal-1C2S and Gal-8N also demonstrated the appearance of higher binding signals, resulting in low
KD values for SNAP-tag harboring proteins (
Figure 5,
Table 3) and indicated that the effect is not restricted to the Gal-3 as representative of the chimera-type class. In the case of Gal-1C2S, we observed similar curve progressions for HSDsRedMGal-1C2S and HSGal-1C2S (
Figure 5A). The red fluorescent protein DsRedM only occurs as a monomeric protein [
67] and thus underlines the probable involvement of the SNAP-tag. However, eGFP can form weak dimers [
68], similar to eYFP, which points out the likely influence on the high binding signal of HSeGFPGal-8N compared to HSGal-8N (
Figure 5B). Furthermore, we observed lower affinities for fusion proteins with a fluorescent protein (HDsRedMGal-1CS and HeGFPGal-8N) compared to the His
6-tagged galectins (HGal-1C2S and HGal-8N) (
Table 3). This indicates a deterioration of the galectins’ binding properties in the fluorescent proteins’ presence. The fusion to SNAP-tag then again enhanced the binding in the assay on ASF, demonstrating the SNAP-tag’s contribution. We conclude that the SNAP-tag limits the use of the galectin fusion proteins in ELISA/ELLA type assays with higher absolute read out and apparent lower
KD values.
Considering the likely oligomerization of the fusion protein HSYGal-3 by the SNAP-tag, we compared the binding properties of Gal-3 proteins HGal-3 and HSYGal-3 to naturally occurring ECM glycoproteins laminin, fibronectin, and collagen IV (
Figure 6). Galectins located in the extracellular space mediate cell-cell or cell-matrix interactions by crosslinking glycoproteins of the cell surface and ECM [
3,
4]. For both Gal-3 proteins, we detected binding to these glycoconjugates, which is in good agreement with former studies on Gal-3 and the tested ECM glycoproteins [
22,
47,
48,
49,
69,
70,
71,
72]. For HGal-3, the screening revealed graded affinities for the ECM proteins, with laminin as the best ligand with
KD values in the submicromolar range, followed by fibronectin and collagen IV (
Table 4). The high affinity of Gal-3 towards laminin is due to the high number of poly-
N-acetyllactosamine-terminated N-glycans presented on this heterotrimeric ECM glycoprotein which is a preferred ligand for Gal-3 [
73,
74,
75,
76]. Furthermore, Gal-3 can bind internal galactose residues [
51]. On the contrary, fibronectin mainly presents sialylated N-glycans consisting of one lactosamine unit [
75,
77]. Although collagen IV is a major structural component of the extracellular space, it is modified only with galactosyl-hydroxylysine and glucosyl-galactosyl-hydroxylysine residues and, therefore, the least preferred ligand for Gal-3 [
78,
79]. The fusion protein HSYGal-3 displayed lower
KD values than HGal-3 but without differentiation between the ECM proteins (
Table 4). We also obtained the same effect in the ECM binding studies for Gal-1C2S and Gal-8N (
Figure S17 and
Table 4). Furthermore, these findings correlate with previously performed experiments with the galectin fusion proteins in the binding assays with ASF (
Figure 3 and 4). The probable oligomerization of the fusion proteins by the SNAP-tag under the given conditions in the microtiter plate leads to higher binding signals. Thus, using different ECM glycoproteins and the comparison to HGal-3 demonstrate that the high affinities of the fusion protein HSYGal-3 and other galectin fusion proteins do not reflect the natural affinity of the Gal-3 domain. These results further confirm our conclusion that the binding affinity of SNAP-tag galectin fusion proteins in ELISA type assays should be carefully discussed.
The ability of galectins to bind glycoproteins and simultaneously form oligomers enables the crosslinking and adhesion of different cells or cell-matrix components in the extracellular space [
3,
4,
80]. In former studies, we demonstrated the ability of the Gal-3 fusion protein HSYGal-3 to crosslink laminin with an ASF layer by binding laminin to ASF-bound galectins [
22]. Based on this, we have expanded the ECM spectrum and confirmed the crosslinking ability of HGal-3 and HSYGal-3 towards laminin, fibronectin, and collagen IV (
Figure S18), which is due to the ability of Gal-3 to form higher multimers in the presence of multivalent ligands [
45]. We then compared the laminin crosslinking ability of His
6-tagged and fusion proteins of galectin representatives from different galectin classes. Here, we obtained a significant difference in binding and affinity for laminin between the His
6-tagged and the fusion protein of Gal-8N (
Figure 7C and
Table 5). We conclude that chimera-type Gal-3 (
Figure 7A) and proto-type Gal-1C2S (
Figure 7B) have crosslinking activity and assume the oligomerization effect by the SNAP-tag is covered in the crosslinking assay due to the natural oligomerization behavior of these galectins. Gal-3 forms higher oligomers up to pentamers which are mediated by the glycine- and proline-rich N-terminal region, whereas Gal-1C2S is a non-covalent homodimeric protein [
45,
81,
82]. The SNAP-tag may further trigger oligomerization and crosslinking ability. It is also reported that Gal-8 probably exists as a dimer through the interaction of the N-terminal domain [
83]. Thus, the significant difference within the
KD values of the HGal-8N and HSeGFPGal-8N (
Table 5) may be traced back to the non-preference of Gal-8N for poly-LacNAc glycans and, on the other side, it may be attributed to the SNAP-tag fusion inducing aggregation on the ASF layer. We conclude that the SNAP-tag-induced oligomerization benefits the crosslinking properties of galectin fusion proteins.