Function of the propeptide region in recombinant expression of active procathepsin L in Escherichia coli

Structural insights into the psychrophilic germinal protease PaGPR and its autoinhibitory loop

In spore forming microbes, germination protease (GPR) plays a key role in the initiation of the germination process. A critical step during germination is the degradation of small acid-soluble proteins (SASPs), which protect spore DNA from external stresses (UV, heat, low temperature, etc.). Inactive zymogen GPR can be activated by autoprocessing of the N-terminal pro-sequence domain. Activated GPR initiates the degradation of SASPs; however, the detailed mechanisms underlying the activation, catalysis, regulation, and substrate recognition of GPR remain elusive. In this study, we determined the crystal structure of GPR from Paenisporosarcina sp. TG-20 (PaGPR) in its inactive form at a resolution of 2.5 A. Structural analysis showed that the active site of PaGPR is sterically occluded by an inhibitory loop region (residues 202-216). The N-terminal region interacts directly with the self-inhibitory loop region, suggesting that the removal of the N-terminal pro-sequence induces conformational changes, which lead to the release of the self-inhibitory loop region from the active site. In addition, comparative sequence and structural analyses revealed that PaGPR contains two highly conserved Asp residues (D123 and D182) in the active site, similar to the putative aspartic acid protease GPR from Bacillus megaterium. The catalytic domain structure of PaGPR also shares similarities with the sequentially non-homologous proteins HycI and HybD. HycI and HybD are metal-loproteases that also contain two Asp (or Glu) residues in their active site, playing a role in metal binding. In summary, our results provide useful insights into the activation process of PaGPR and its active conformation.

Heterologous expression of the plant cysteine protease bromelain and its inhibitor in Pichia pastoris

Expression of proteases in heterologous hosts remains an ambitious challenge due to severe problems associated with digestion of host proteins. On the other hand, proteases are broadly used in industrial applications and resemble promising drug candidates. Bromelain is an herbal drug that is medicinally used for treatment of oedematous swellings and inflammatory conditions and consists in large part of proteolytic enzymes. Even though various experiments underline the requirement of active cysteine proteases for biological activity, so far no investigation succeeded to clearly clarify the pharmacological mode of action of bromelain. The potential role of proteases themselves and other molecules of this multi-component extract currently remain largely unknown or ill defined. Here, we set out to express several bromelain cysteine proteases as well as a bromelain inhibitor molecule in order to gain defined molecular entities for subsequent studies. After cloning the genes from its natural source Ananas comosus (pineapple plant) into Pichia pastoris and subsequent fermentation and purification, we obtained active protease and inhibitor molecules which were subsequently biochemically characterized. Employing purified bromelain fractions paves the way for further elucidation of pharmacological activities of this natural product. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:54-65, 2017.

A Rhipicephalus (Boophilus) microplus cathepsin with dual peptidase and antimicrobial activity

The cattle tick, Rhipicephalus (Boophilus) microplus, is a haematophagous arthropod responsible for considerable losses in the livestock industry. Immunological control with vaccines is a promising alternative to replace chemical acaricides. Due to their importance in parasite physiology, cysteine endopeptidases are potential targets. In a previous study, native Vitellin Degrading Cysteine Endopeptidase (VTDCE) was successfully tested as a vaccine antigen for bovines against R. microplus. In this work, nucleotide and amino acid VTDCE sequences were obtained from cDNA databanks, based on data from Edman sequencing and mass spectrometry. Subsequently, cloning and expression, purification, immunological and biochemical characterisation of the recombinant protein were performed to determine the biological importance of VTDCE. By Western blot, polyclonal antibodies produced against recombinant VTDCE recognised native VTDCE. Interestingly, molecular analysis showed that the VTDCE sequence has similarity to antimicrobial peptides. Indeed, experimental results revealed that VTDCE has an antimicrobial activity which is independent of endopeptidase activity. We believe that this is the first known study to show that an arthropod enzyme has antimicrobial activity.

Insights from bacterial subtilases into the mechanisms of intramolecular chaperone-mediated activation of furin

Prokaryotic subtilisins and eukaryotic proprotein convertases (PCs) are two homologous protease subfamilies that belong to the larger ubiquitous super-family called subtilases. Members of the subtilase super-family are produced as zymogens wherein their propeptide domains function as dedicated intramolecular chaperones (IMCs) that facilitate correct folding and regulate precise activation of their cognate catalytic domains. The molecular and cellular determinants that modulate IMC-dependent folding and activation of PCs are poorly understood. In this chapter we review what we have learned from the folding and activation of prokaryotic subtilisin, discuss how this has molded our understanding of furin maturation, and foray into the concept of pH sensors, which may represent a paradigm that PCs (and possibly other IMC-dependent eukaryotic proteins) follow for regulating their biological functions using the pH gradient in the secretory pathway.

Production of congopain, the major cysteine protease of Trypanosoma (Nannomonas) congolense, in Pichia pastoris reveals unexpected dimerisation at physiological pH

African animal trypanosomosis (nagana) is arguably the most important parasitic disease affecting livestock in sub-Saharan Africa. Since none of the existing control measures are entirely satisfactory, vaccine development is being actively pursued. However, due to antigenic variation, the quest for a conventional vaccine has proven elusive. As a result, we have sought an alternative 'anti-disease vaccine approach', based on congopain, a cysteine protease of Trypanosoma congolense, which was shown to have pathogenic effects in vivo. Congopain was initially expressed as a recombinant protein in bacterial and baculovirus expression systems, but both the folding and yield obtained proved inadequate. Hence alternative expression systems were investigated, amongst which Pichia pastoris proved to be the most suitable. We report here the expression of full length, and C-terminal domain-truncated congopain in the methylotrophic yeast P. pastoris. Differences in yield were observed between full length and truncated proteins, the full length producing 2-4 mg of protein per litre of culture, while the truncated form produced 20-30 mg/l. The protease was produced as a proenzyme, but underwent spontaneous activation when acidified (pH <5). To investigate whether this activation was due to autolysis, we produced an inactive mutant (active site Cys→Ala) by site-directed mutagenesis. The mutant form was produced at a much higher rate, up to 100mg/l culture, as a proenzyme. It did not undergo spontaneous cleavage of the propeptide when subjected to acidic pH suggesting an autocatalytic process of activation for congopain. These recombinant proteins displayed a very unusual feature for cathepsin L-like proteinases, i.e. complete dimerisation at pH >6, and by reversibly monomerising at acidic pH <5. This attribute is of utmost importance in the context of an anti-disease vaccine, given that the epitopes recognised by the sera of trypanosome-infected trypanotolerant cattle appear dimer-specific.

A heparin binding motif on the pro-domain of human procathepsin L mediates zymogen destabilization and activation

The molecular mechanism by which heparin modulates the processing of procathepsin L in the extracellular environment is proposed. We show that heparin reduces the stability of the pro form of cathepsin L at pH 5 by binding to a putative heparin binding motif (BBXB) in the pro-domain. Mutations to this motif on procathepsin L reduce heparin binding affinity and heparin-induced destabilization; in contrast, heparin only slightly destabilizes the mature cathepsin L domain. Gel analysis further shows that heparin makes procathepsin L a much better substrate for cathepsin L. Thus, heparin enhances the rate of zymogen activation by destabilization upon binding to the BBXB motif. Determining the mechanism by which procathepsin L is activated in the extracellular matrix is important to the understanding of the role that cathepsin L plays in tumour invasion.

Optimized folding and activation of recombinant procathepsin L and S produced in Escherichia coli

Large scale production of the recombinant human cathepsins L and S was optimized. Final purity was nearly 100%, yield 65% and 41%, respectively. Cost-effective expression in Escherichia coli, inclusion body purification and solubilization followed modified standard protocols. Most contribution to the remarkable increase in over-all efficiency came from the subsequent steps: folding by dilution, selective HIC-capturing of the folded proenzymes, and auto-activation. The effort to optimize the process parameters for folding and activation was greatly reduced by central composite fractional factorial experimental design, considering curved responses as well as factor interactions. Theoretical and practical features of this powerful tool for experimental design are given. Yield in procathepsin S folding could be further increased by addition of an excess of its own native propeptide with known intramolecular chaperone function. This corroborates literature data on proenzyme folding and is broadly discussed in the light of the lower conformational stability of the prodomain compared to the catalytic unit. Auto-activation kinetics was largely different between the two related proenzymes; from its time course contribution of uni- and bimolecular events in proregion hydrolysis and rate constants were estimated.

Cowpea bruchid Callosobruchus maculatus counteracts dietary protease inhibitors by modulating propeptides of major digestive enzymes

Cowpea bruchids, when challenged by consumption of the soybean cysteine protease inhibitor scN, reconfigure expression of their major CmCP digestive proteases and resume normal feeding and development. Previous evidence indicated that insects selectively induced CmCPs from subfamily B, that were more efficient in autoprocessing and possessed not only higher proteolytic, but also scN-degrading activities. In contrast, dietary scN only marginally up-regulated genes from the more predominant CmCP subfamily A that were inferior to subfamily B. To gain further molecular insight into this adaptive adjustment, we performed domain swapping between the two respective subfamily members B1 and A16, the latter unable to autoprocess or degrade scN even after intermolecular processing. Swapping the propeptides did not qualitatively alter autoprocessing in either protease isoform. Incorporation of either the N- (pAmBA) or C-terminal (pAmAB) mature B1 segment into A16, however, was sufficient to prime autoprocessing of A16 to its mature form. Further, the swap at the N-terminal mature A16 protein region (pAmBA) resulted in four amino acid changes. Replacement of these amino acid residues by the corresponding B1 residues, singly and pair-wise, revealed that autoprocessing activation in pAmBA resulted from cumulative and/or coordinated individual effects. Bacterially expressed isolated propeptides (pA16 and pB1) differed in their ability to inhibit mature B1 enzyme. Lower inhibitory activity in pB1 is likely attributable to its lack of protein stability. This instability in the cleaved propeptide is necessary, although insufficient by itself, for scN-degradation by the mature B1 enzyme. Taken together, cowpea bruchids modulate proteolysis of their digestive enzymes by controlling proCmCP cleavage and propeptide stability, which explains at least in part the plasticity cowpea bruchids demonstrate in response to protease inhibitors.

The major secreted cathepsin L1 protease of the liver fluke, Fasciola hepatica: a Leu-12 to Pro-12 replacement in the nonconserved C-terminal region of the prosegment prevents complete enzyme autoactivation and allows definition of the molecular events in prosegment removal

A protease secreted by the parasitic helminth Fasciola hepatica, a 37-kDa procathepsin L1 (FheproCL1), autocatalytically processes and activates to its mature enzyme (FheCL1) over a wide pH range of 7.3 to 4.0, although activation is more rapid at low pH. Maturation initiates with cleavages of a small proportion of molecules within the central region of the prosegment, possibly by intramolecular events. However, activation to fully mature enzymes is achieved by a precise intermolecular cleavage at a Leu-12-Ser-11 downward arrowHis-10 sequence within the nonconserved C-terminal region of the prosegment. The importance of this cleavage site in enzyme activation was demonstrated using an active site variant FheproCL1Gly26 (Cys26 to Gly26) and a double variant FheproCL1Pro-12/Gly26 (Leu-12 to Pro-12), and although both of these variants cannot autocatalytically process, the former is susceptible to trans-processing at a Leu-12-Ser-11 downward arrowHis-10 sequence by pre-activated FheCL1, but the latter is not. Another F. hepatica secreted protease FheCL2, which, unlike FheCL1, can readily accept proline in the S2 subsite of its active site, can trans-process the double variant FheproCL1Pro-12/Gly26 by cleavage at the Pro-12-Ser-11 downward arrowHis-10 sequence. Furthermore, the autoactivation of a variant enzyme with a single replacement, FheproCL1Pro-12, was very slow but was increased 40-fold in the presence of FheCL2. These studies provide a molecular insight into the regulation of FheproCL1 autocatalysis.

The crystal structure of a Cys25 -> Ala mutant of human procathepsin S elucidates enzyme-prosequence interactions

The crystal structure of the active-site mutant Cys25 --> Ala of glycosylated human procathepsin S is reported. It was determined by molecular replacement and refined to 2.1 Angstrom resolution, with an R-factor of 0.198. The overall structure is very similar to other cathepsin L-like zymogens of the C1A clan. The peptidase unit comprises two globular domains, and a small third domain is formed by the N-terminal part of the prosequence. It is anchored to the prosegment binding loop of the enzyme. Prosegment residues beyond the prodomain dock to the substrate binding cleft in a nonproductive orientation. Structural comparison with published data for mature cathepsin S revealed that procathepsin S residues Phe146, Phe70, and Phe211 adopt different orientations. Being part of the S1' and S2 pockets, they may contribute to the selectivity of ligand binding. Regarding the prosequence, length, orientation and anchoring of helix alpha3p differ from related zymogens, thereby possibly contributing to the specificity of propeptide-enzyme interaction in the papain family. The discussion focuses on the functional importance of the most conserved residues in the prosequence for structural integrity, inhibition and folding assistance, considering scanning mutagenesis data published for procathepsin S and for its isolated propeptide.

Functional roles of specific bruchid protease isoforms in adaptation to a soybean protease inhibitor

Upon challenge by the soybean cysteine protease inhibitor soyacystatin N (scN), cowpea bruchids reconfigure their major digestive cysteine proteases (CmCPs) in adaptation to the inhibitor and resume normal feeding and development. We have previously shown that CmCPB transcripts were 116.3-fold more abundant in scN-adapted bruchid guts than in unadapted guts, while CmCPA transcripts were only 2.5-fold higher. In order to further elucidate the functional significance of this differential regulation, we expressed three CmCPA and one CmCPB isoforms (A9, A13, A16 and B1) using a bacterial expression system, and characterized their activities. In contrast to the precursors of CmCPAs (proCmCPAs), proCmCPB1 exhibited more efficient autocatalytic conversion from the latent proenzyme to its active mature protease form, and demonstrated higher intrinsic proteolytic activity. Among proCmCPAs, dependence on exogenous enzymatic processing varies: while maturation of proCmCPA13 and proCmCPA16 was impaired in the absence of external proteolytic activity, proCmCPA9 appeared to utilize a two-step autoprocessing mechanism. Although all CmCPs are scN-sensitive, scN was degraded by CmCPB1 when outnumbered by the protease, but scN remained intact in the presence of excessive CmCPA9. These results provide further evidence that differential expression of CmCPs under scN challenge brings about adaptation to the inhibitor. High induction of unique cysteine protease isoforms with superior autoprocessing and proteolytic efficacy represents a strategy cowpea bruchids use to cope with dietary scN.

Cathepsin L1, the Major Protease Involved in Liver Fluke (Fasciola hepatica) Virulence

The secretion and activation of the major cathepsin L1 cysteine protease involved in the virulence of the helminth pathogen Fasciola hepatica was investigated. Only the fully processed and active mature enzyme can be detected in medium in which adult F. hepatica are cultured. However, immunocytochemical studies revealed that the inactive procathepsin L1 is packaged in secretory vesicles of epithelial cells that line the parasite gut. These observations suggest that processing and activation of procathepsin L1 occurs following secretion from these cells into the acidic gut lumen. Expression of the 37-kDa procathepsin L1 in Pichia pastoris showed that an intermolecular processing event within a conserved GXNXFXD motif in the propeptide generates an active 30-kDa intermediate form. Further activation of the enzyme was initiated by decreasing the pH to 5.0 and involved the progressive processing of the 37 and 30-kDa forms to other intermediates and finally to a fully mature 24.5 kDa cathepsin L with an additional 1 or 2 amino acids. An active site mutant procathepsin L, constructed by replacing the Cys(26) with Gly(26), failed to autoprocess. However, [Gly(26)]procathepsin L was processed by exogenous wild-type cathepsin L to a mature enzyme plus 10 amino acids attached to the N terminus. This exogenous processing occurred without the formation of a 30-kDa intermediate form. The results indicate that activation of procathepsin L1 by removal of the propeptide can occur by different pathways, and that this takes place within the parasite gut where the protease functions in food digestion and from where it is liberated as an active enzyme for additional extracorporeal roles.

A critical review of the methods for cleavage of fusion proteins with thrombin and factor Xa

Expression and purification of proteins in recombinant DNA systems is a powerful and widely used technique. Frequently there is the need to express the protein of interest as a fusion protein or chimeric protein. Fusion protein technology is frequently used to attach a "signal" which can be used for subsequent localization of the protein or a "carrier" which can be used to deliver a "therapeutic" such as a radioactive molecule to a specific site. In addition to these applications, fusion protein technology can be employed for several other useful purposes. Of these, the most frequent reason is to provide a 'tag' or 'handle' which will aid in the purification of the protein. Another useful purpose is to improve the expression or folding of the protein of interest. In these latter two situations, it is often necessary to remove the fusion partner before the recombinant protein of interest can be used for further studies. This removal process involves the insertion of a unique amino acid sequence that is susceptible to cleavage by a highly specific protease. Thrombin and factor Xa are the most frequently used proteases for this application. The purpose of this review is to discuss the application of thrombin and factor Xa for the cleavage of fusion proteins. It is emphasized that while these enzymes are quite specific for cleavage at the inserted cleavage site, proteolysis can frequently occur at other site(s) in the protein of interest. It is necessary to characterize the protein of interest after cleavage from the affinity label to assure that there are no changes in the covalent structure of the protein of interest. Examples are presented which describe the proteolysis of the protein of interest by either factor Xa or thrombin.

Foldase function of the cathepsin S proregion is strictly based upon its domain structure

Folding of cathepsin S, like other cathepsin L-like proteases, depends on its proregion. The major part of the proregion forms a small domain distal from the catalytic centre, suggesting function(s) beyond active-site shielding. Using an optimised in vitro trans-refolding assay, we compared reactivation of denatured cathepsin S by the genuine propeptide, wild-type and ten selected mutants. Including structural data and binding constants, we identified the prodomain core and the hairpin region to be important for the foldase function.

Identification of in vitro folding conditions for procathepsin S and cathepsin S using fractional factorial screens

Human procathepsin S and cathepsin S were expressed as inclusion bodies in Escherichia coli. Following solubilization of the inclusion body proteins, fractional factorial protein folding screens were used to identify folding conditions for procathepsin S and cathepsin S. A primary folding screen, including eight factors each at two levels, identified pH and arginine as the main factors affecting procathepsin S folding. In a second simple screen, the yields were further improved. The in vitro folding of mature cathepsin S has never been reported previously. In this study we used a series of fractional factorial screens to identify conditions that enabled the active enzyme to be generated without the prodomain although the yields were much lower than achieved with procathepsin S. Our data show the power of fractional factorial screens to rapidly identify folding conditions even for a protein that does not easily fold into its active conformation.

The residual pro-part of cathepsin C fulfills the criteria required for an intramolecular chaperone in folding and stabilizing the human proenzyme

The 13.5 kDa N-terminal part of the propeptide remains associated with mature cathepsin C after proteolytic activation and excision of the activation peptide. This residual pro-part, isolated from the recombinant enzyme, folds spontaneously and rapidly to a stable, compact monomer with secondary structure and stable tertiary interactions. Folding and unfolding kinetics of the residual pro-part with intact disulfides are complex, and accumulation of transient intermediates is observed. The cleaved form of the pro-part isolated from natural human cathepsin C also folds, suggesting that the intact form comprises two folding domains. The linkages of the two disulfide bridges have been established as 30-118 and 54-136 for the native enzyme. The native disulfide bonds can be re-formed from the fully reduced and denatured state by oxidative refolding, resulting in a domain that is spectroscopically indistinguishable from the original refolded residual pro-part. Both disulfides are solvent-exposed and can be reduced in the absence of denaturant. The reduced form retains most or all of the native tertiary structure and is only approximately 2 kcal.mol(-1) less stable than the oxidized form. It folds fast relative to the rate of biosynthesis, to the same conformation as the oxidized form. Folding and disulfide formation are sequential. These results indicate that the proenzyme folds sequentially in vivo and that the residual pro-part constitutes a rapidly and independently folding domain that stabilizes the mature enzyme. It thus fulfills the criteria required of an intramolecular chaperone. It may also be involved in stabilizing the tetrameric structure of the mature enzyme.