SlyD Protein Research Articles

A novel epitope-presenting thermostable scaffold for the development of highly specific insulin-like growth factor-1/2 antibodies

High sequence and structural homology between mature human insulin-like growth factors IGF-1 and IGF-2 makes serological discrimination by immunodiagnostic IGF tests a challenging task. There is an urgent need for highly specific IGF-1 and IGF-2 antibodies, yet only a short sequence element, i.e. the IGF loop, provides enough difference in sequence to discriminate between the two molecules. We sought to address this unmet demand by investigating novel chimeric immunogens as carriers for recombinant peptide motif grafting. We found Thermus thermophilus sensitive to lysis D (SlyD) and Thermococcus gammatolerans SlyD FK-506–binding protein (FKBP) domains suitable for presentation of the predefined epitopes, namely the IGF-1 and IGF-2 loops. Chimeric SlyD-IGF proteins allowed for the development of exceptionally specific IGF-1 and IGF-2 monoclonal antibodies. The selected antibodies bound with high affinity to the distinct IGF epitopes displayed on the protein scaffolds, as well as on the mature human IGF isoforms. The respective SlyD scaffolds display favorable engineering properties in that they are small, monomeric, and cysteine-free and can be produced in high yields in a prokaryotic host, such as Escherichia coli. In conclusion, FKBP domains from thermostable SlyD proteins are highly suitable as a generic scaffold platform for epitope grafting.

Generation of Nanobodies against SlyD and development of tools to eliminate this bacterial contaminant from recombinant proteins

The gene for a protein domain, derived from a tumor marker, fused to His tag codons and under control of a T7 promotor was expressed in E. coli strain BL21 (DE3). The recombinant protein was purified from cell lysates through immobilized metal affinity chromatography and size-exclusion chromatography. A contaminating bacterial protein was consistently co-purified, even using stringent washing solutions containing 50 or 100 mM imidazole. Immunization of a dromedary with this contaminated protein preparation, and the subsequent generation and panning of the immune Nanobody library yielded several Nanobodies of which 2/3 were directed against the bacterial contaminant, reflecting the immunodominance of this protein to steer the dromedary immune response. Affinity adsorption of this contaminant using one of our specific Nanobodies followed by mass spectrometry identified the bacterial contaminant as FKBP-type peptidyl-prolyl cis-trans isomerase (SlyD) from E. coli. This SlyD protein contains in its C-terminal region 14 histidines in a stretch of 31 amino acids, which explains its co-purification on Ni-NTA resin. This protein is most likely present to varying extents in all recombinant protein preparations after immobilized metal affinity chromatography. Using our SlyD-specific Nb 5 we generated an immune-complex that could be removed either by immunocapturing or by size exclusion chromatography. Both methods allow us to prepare a recombinant protein sample where the SlyD contaminant was quantitatively eliminated.

Dynamic control of the prolyl isomerase function of the dual-domain SlyD protein

Local dynamics on variable timescales are important to facilitate high catalytic efficiency in enzymes. In this study, we examined the dual-domain peptidyl-prolyl cis/trans-isomerase (PPIase) SlyD with regard to its catalytic cycle. Fluorescence- and NMR-based experiments were performed to understand the high catalytic efficiency of SlyD compared to single domain FKBP proteins. We probed local conformational changes for amino acids involved in substrate-binding (IF domain) and substrate-catalysis (FKBP domain) taking place on the timescale of substrate turnover. Binding of the PPIase activity inhibitors to the FKBP domain suppressed the conformational freedom of the remote IF domain. A single side-chain mutation in the active site strongly reduced the rate of substrate turnover and changed the conformational dynamics of all amino acids involved in catalysis. This dynamic interplay between substrate-binding domain and PPIase domain determines the high catalytic activity of SlyD and inhibitor-binding modulates the backbone plasticity required for enzyme activity.

2PT144 SlyD融合による人工三本鎖ベータヘリックスの可溶化の試み(日本生物物理学会第50回年会(2012年度))

2PT144 SlyD融合による人工三本鎖ベータヘリックスの可溶化の試み(日本生物物理学会第50回年会(2012年度))

Coordination of Ni 2 + and Cu 2 + to metal ion binding domains of E. coli SlyD protein

The C-terminal region of Escherichia coli SlyD is unstructured and extremely rich in potential metal-binding amino acids, especially in histidine residues. SlyD is able to bind two to seven nickel ions per molecule, in a variety of coordination geometries and coordination numbers. This protein contributes to the insertion of nickel into the hydrogenase precursor protein and it has a peptidyl-prolyl cis/trans-isomerase activity which can be regulated through nickel ions. This inspired us to undertake systematic studies on the coordination ability of two histidine-rich peptides from the C-terminus of the SlyD protein with nickel. Also, it is known that histidine-rich regions are part of a Cu 2 + binding domain involved in copper uptake under conditions of metal starvation in vivo in other bacteria. For this reason we decided to examine the complex formation of Ac-AHGHVHGAHDHHHD-NH 2 and Ac-GHGHDHGHEHG-NH 2 fragments with copper ions, which are also reference metal ions in this study. Experiments were performed in a DMSO/water 30:70 solvent. The Ac-AHGHVHGAHDHHHD-NH 2 and Ac-GHGHDHGHEHG-NH 2 fragments were synthesized and their interactions with Ni 2 + and Cu 2 + ions were studied by potentiometric, mass spectrometric, UV–vis, CD, EPR, and NMR spectroscopic techniques in solution. The results show that the Ac-GHGHDHGHEHG-NH 2 fragment forms equimolar complexes with both nickel and copper ions. At physiological pH, the metal ion is bound only through nitrogens from imidazole sidechain of histidine residues. On the contrary, Ac-AHGHVHGAHDHHHD-NH 2 binds 2 metal ions per molecule, at pH range 5 to 7, even if the 1:2 metal:peptide ratios were used. NMR studies indicate the involvement of all His residues in this pH-range in metal binding of the latter peptide. At higher pH, the stoichiometry changes to 1:1 and the His residues are displaced by amide nitrogens.

Insertion of a Chaperone Domain Converts FKBP12 into a Powerful Catalyst of Protein Folding

The catalytic activity of human FKBP12 as a prolyl isomerase is high towards short peptides, but very low in proline-limited protein folding reactions. In contrast, the SlyD proteins, which are members of the FKBP family, are highly active as folding enzymes. They contain an extra “insert-in-flap” or IF domain near the prolyl isomerase active site. The excision of this domain did not affect the prolyl isomerase activity of SlyD from Escherichia coli towards short peptide substrates but abolished its catalytic activity in proline-limited protein folding reactions. The reciprocal insertion of the IF domain of SlyD into human FKBP12 increased its folding activity 200-fold and generated a folding catalyst that is more active than SlyD itself. The IF domain binds to refolding protein chains and thus functions as a chaperone module. A prolyl isomerase catalytic site and a separate chaperone site with an adapted affinity for refolding protein chains are the key elements for a productive coupling between the catalysis of prolyl isomerization and conformational folding in the enzymatic mechanisms of SlyD and other prolyl isomerases, such as trigger factor and FkpA.

SlyD Proteins from Different Species Exhibit High Prolyl Isomerase and Chaperone Activities

SlyD is a putative folding helper protein from the Escherichia coli cytosol, which consists of an N-terminal prolyl isomerase domain of the FKBP type and a presumably unstructured C-terminal tail. We produced truncated versions without this tail (SlyD) for SlyD from E. coli, as well as for the SlyD orthologues from Yersinia pestis, Treponema pallidum, Pasteurella multocida, and Vibrio cholerae. They are monomeric in solution and unfold reversibly. All SlyD variants catalyze the proline-limited refolding of ribonuclease T1 with very high efficiencies, and the specificity constants (kcat/KM) are equal to approximately 10(6) M(-1) s(-1). These large values originate from the high affinities of the SlyD orthologues for unfolded RCM-T1, which are reflected in low KM values of approximately 1 microM. SlyD also exhibits pronounced chaperone properties. Permanently unfolded proteins bind with high affinity to SlyD and thus inhibit its prolyl isomerase activity. The unfolded protein chains do not need to contain proline residues to be recognized and bound by SlyD. The conservation of prolyl isomerase activity and chaperone properties within the SlyD family suggests that these proteins might act as true folding helpers in the bacterial cytosol. The SlyD proteins are also well suited for biotechnological applications. As fusion partners they facilitate the refolding and increase the solubility of aggregation-prone proteins such as the gp41 ectodomain fragment of HIV-1.

The Regulation of Type 7 Adenylyl Cyclase by Its C1b Region and Escherichia coli Peptidylprolyl Isomerase, SlyD

Mammalian membrane-bound adenylyl cyclase consists of two highly conserved cytoplasmic domains (C1a and C2a) separated by a less conserved connecting region, C1b, and one of two transmembrane domains, M2. The C1a and C2a domains form a catalytic core that can be stimulated by forskolin and the stimulatory G protein subunit alpha (Galpha(s)). In this study, we analyzed the regulation of type 7 adenylyl cyclase (AC7) by C1b. The C1a, C1b, and C2a domains of AC7 were purified separately. Escherichia coli SlyD protein, a cis-trans peptidylprolyl isomerase (PPIase), copurifies with AC7 C1b (7C1b). SlyD protein can inhibit the Galpha(s)- and/or forskolin-activated activity of both soluble and membrane-bound AC7. Mutant forms of SlyD with reduced PPIase activity are less potent in the inhibition of AC7 activity. Interestingly, different isoforms of mammalian membrane-bound adenylyl cyclase can be either inhibited or stimulated by SlyD protein, raising the possibility that mammalian PPIase may regulate enzymatic activity of mammalian adenylyl cyclase. Purified 7C1b-SlyD complex has a greater inhibitory effect on AC7 activity than SlyD alone. This inhibition by 7C1b is abolished in a 7C1b mutant in which a conserved glutamic acid (amino acid residue 582) is changed to alanine. Inhibition of adenylyl cyclase activity by 7C1b is further confirmed by using 7C1b purified from an E. coli slyD-deficient strain. This inhibitory activity of AC7 is also observed with the 28-mer peptides derived from a region of C1b conserved in AC7 and AC2 but is not observed with a peptide derived from the corresponding region of AC6. This inhibitory activity exhibited by the C1b domain may result from the interaction of 7C1b with 7C1a and 7C2a and may serve to hold AC7 in the basal nonstimulated state.

Cloning and characterization of two immunophilin-like genes, ilpA and fkpA, on a single 3.9-kilobase fragment of Aeromonas hydrophila genomic DNA.

Antiserum to Aeromonas hydrophila A6 cell envelopes was shown in a previous study (C. Y. F. Wong, G. Mayrhofer, M. W. Heuzenroeder, H. M. Atkinson, D. M. Quinn, and R. L. P. Flower, FEMS Immunol. Med. Microbiol. 15:233-241, 1996) to protect mice against lethal infection by this organism. In this study, colony blot analysis of an A. hydrophila genomic library using antiserum to A. hydrophila A6 cell envelopes revealed a cosmid clone expressing a 30-kDa protein which has not been described previously in aeromonads. The nucleotide sequence of a 3.9-kb fragment derived from this cosmid which expressed the 30-kDa protein revealed two potential open reading frames (ORFs) with homology to known immunophilin proteins. ORF1 encoded a 212-amino-acid protein (molecular mass, 22.4 kDa) with 56% identity to the immunophilin SlyD protein of Escherichia coli. ORF1 was subsequently designated ilpA (immunophilin-like protein). ORF3 encoded a potential gene product of 268 amino acids with a typical signal sequence and a predicted molecular size of 28.7 kDa. The inferred amino acid sequence showed 46% identity with the sequence of the FkpA protein of E. coli and 40% identity with the sequence of the macrophage infectivity potentiator (Mip) protein of Legionella pneumophila. ORF3 was designated fkpA (FK506 binding protein) by analogy with the E. coli FkpA protein. Expression of the FkpA protein was confirmed by Western blot (immunoblot) analysis, which detected a 30-kDa protein, with antiserum to the Mip protein of Legionella longbeachae and a specific antiserum to anA. hydrophila 30-kDa membrane protein. PCR and Southern analysis showed that a DNA sequence encoding FkpA was found in all 178 aeromonads of diverse origins tested. A nonpolar insertion mutation in the fkpA gene did not attenuate virulence in a suckling mouse model nor did it affect the expression of hemolysins or DNase. This suggests that either the fkpA gene is not essential in the virulence of A. hydrophila under these conditions or there are other genes in A. hydrophila coding for proteins with similar functions.

φX174 lysis requires slyD, a host gene which is related to the FKBP family of peptidyl-prolyl cis-trans isomerases

Recessive mutations in the slyD (sensitivity to lysis) gene were isolated by selecting for survival after induction of the cloned lysis gene E of bacteriophage φX174 [1]. The slyD − mutation, transduced into the normal φX174 host, Escherichia coli C, confers an absolute block on the plaque-forming ability of the wild-type phage, indicating that slyD is required for E function. slyD encodes a protein with 196 residues. A segment corresponding to the first 142 residues of the predicted SlyD protein has significant similarity throughout its length to the FKBP family of peptidyl-prolyl cis-trans isomerases, or rotamases. The C-terminal 46 codons of slyD encode a remarkable histidine-rich peptide which is a metal-binding domain [2]. This sequence is dispensable for slyD function in E-mediated lysis. Although there is no obvious phenotype associated with the slyD − genotype other than the resistance to E-mediated lysis, overexpression of slyD causes cells to filament and to increase significantly in diameter. Mutations in φX174 can restore the plaque-forming ability of the phage on a slyD − host. These pos ( plates on slyD) mutants plate on E. coli C wild-type and slyD −. A model for SlyD involvement in E function and the role of SlyD in the cell is discussed.

Phi X174 lysis requires slyD, a host gene which is related to the FKBP family of peptidyl-prolyl cis-trans isomerases.

Recessive mutations in the slyD (sensitivity to lysis) gene were isolated by selecting for survival after induction of the cloned lysis gene E of bacteriophage phi X174 [1]. The slyD- mutation, transduced into the normal phi X174 host, Escherichia coli C, confers an absolute block on the plaque-forming ability of the wild-type phage, indicating that slyD is required for E function. slyD encodes a protein with 196 residues. A segment corresponding to the first 142 residues of the predicted SlyD protein has significant similarity throughout its length to the FKBP family of peptidyl-prolyl cis-trans isomerases, or rotamases. The C-terminal 46 codons of slyD encode a remarkable histidine-rich peptide which is a metal-binding domain [2]. This sequence is dispensable for slyD function in E-mediated lysis. Although there is no obvious phenotype associated with the slyD- genotype other than the resistance to E-mediated lysis, overexpression of slyD causes cells to filament and to increase significantly in diameter. Mutations in phi X174 can restore the plaque-forming ability of the phage on a slyD- host. These pos (plates on slyD) mutants plate on E. coli C wild-type and slyD-. A model for SlyD involvement in E function and the role of SlyD in the cell is discussed.

SlyD, a host gene required for phi X174 lysis, is related to the FK506-binding protein family of peptidyl-prolyl cis-trans-isomerases.

Recessive mutations in the slyD gene were isolated by selecting for survival after induction of the cloned lysis gene E of bacteriophage phi X174 (Maratea, D., Young, K., and Young, R. (1985) Gene (Amst.) 40, 39-46). The slyD1 mutation, transduced into the normal phi X174 host, Escherichia coli C, confers an absolute block on the plaque-forming ability of the wild-type phage, indicating that slyD is required for E function rather than for expression from the plasmid vector. The cloning, sequencing, and deletion analysis of a 1-kilobase pair genomic fragment containing the slyD locus, mapping at 73.5', is reported. Three reading frames, orf72, orf159, and orf196, are contained within this fragment, with the latter two reading frames occupying the same DNA on opposite strands. Deletion analysis shows that the complementing activity is restricted to the orf159/orf196 DNA. Complementation of the SlyD phenotype was observed irrespective of the orientation of the orf159/orf196 DNA with respect to a vector promoter, indicating that a cryptic promoter serves slyD on this fragment. Using site-directed mutagenesis, nonsense mutations were created in each reading frame which were silent in the opposing frame. Both orf196 nonsense alleles failed to complement slyD1, whereas both orf159 nonsense alleles retained complementation, demonstrating rigorously that orf196 is slyD. A segment corresponding to the first 150 residues of the predicted SlyD protein has significant similarity throughout its length to the FKBP family of peptidyl-prolyl cis-trans-isomerases or rotamases. The COOH-terminal 46 codons of slyD encode a remarkable histidine-rich peptide sequence which is at least partly dispensable for slyD function in E-mediated lysis. Overexpression of slyD in E. coli is toxic. These findings are discussed in terms of a model for SlyD involvement in E function and in terms of a model for SlyD involvement of the ubiquitous FKBP rotamases.