Efficient co-expression of a recombinant staphopain A and its inhibitor staphostatin A in Escherichia coli

Recombinant T7 RNA polymerase production using ClearColi BL21(DE3) and animal-free media for in vitro transcription

In vitro transcription (IVT) using T7 RNA polymerase (RNAP) is integral to RNA research, yet producing this enzyme in E. coli presents challenges regarding endotoxins and animal-sourced toxins. This study demonstrates the viable production and characterization of T7 RNAP using ClearColi BL21(DE3) (an endotoxin-free E. coli strain) and animal-free media. Compared to BL21(DE3) with animal-free medium, soluble T7 RNAP expression is ~50% lower in ClearColi BL21(DE3). Optimal soluble T7 RNAP expression in flask fermentation is achieved through the design of experiments (DoE). Specification and functional testing showed that the endotoxin-free T7 RNAP has comparable activity to conventional T7 RNAP. After Ni-NTA purification, endotoxin levels were approximately 109-fold lower than T7 RNAP from BL21(DE3) with animal-free medium. Furthermore, a full factorial DoE created an optimal IVT system that maximized mRNA yield from the endotoxin-free and animal-free T7 RNAP. This work addresses critical challenges in recombinant T7 RNAP production through innovative host and medium combinations, avoided endotoxin risks and animal-derived toxins. Together with an optimized IVT reaction system, this study represents a significant advance for safe and reliable reagent manufacturing and RNA therapeutics. KEY POINTS: • Optimized IVT system maximizes mRNA yields, enabling the synthesis of long RNAs. • Novel production method yields endotoxin-free and animal-free T7 RNAP. • The T7 RNAP has equivalent specifications and function to conventional T7 RNAP.

Eukaryotic translation initiation factor 5A and its posttranslational modifications play an important role in proliferation and potentially in differentiation of the human enteric protozoan parasite Entamoeba histolytica

The eukaryotic translation initiation factor 5A (eIF5A) is a highly conserved protein and is essential in all eukaryotes. However, the specific roles of eIF5A in translation and in other biological processes remain elusive. In the present study, we described the role of eIF5A, its posttranslational modifications (PTM), and the biosynthetic pathway needed for the PTM in Entamoeba histolytica, the protozoan parasite responsible for amoebic dysentery and liver abscess in humans. E. histolytica encodes two isotypes of eIF5A and two isotypes of enzymes, deoxyhypusine synthase (DHS), responsible for their PTM. Both of the two eIF5A isotypes are functional, whereas only one DHS (EhDHS1, but not EhDHS2), is catalytically active. The DHS activity increased ~2000-fold when EhDHS1 was co-expressed with EhDHS2 in Escherichia coli, suggesting that the formation of a heteromeric complex is needed for full enzymatic activity. Both EhDHS1 and 2 genes were required for in vitro growth of E. histolytica trophozoites, indicated by small antisense RNA-mediated gene silencing. In trophozoites, only eIF5A2, but not eIF5A1, gene was actively transcribed. Gene silencing of eIF5A2 caused compensatory induction of expression of eIF5A1 gene, suggesting interchangeable role of the two eIF5A isotypes and also reinforcing the importance of eIF5As for parasite proliferation and survival. Furthermore, using a sibling species, Entamoeba invadens, we found that eIF5A1 gene was upregulated during excystation, while eIF5A2 was downregulated, suggesting that eIF5A1 gene plays an important role during differentiation. Taken together, these results have underscored the essentiality of eIF5A and DHS, for proliferation and potentially in the differentiation of this parasite, and suggest that the hypusination associated pathway represents a novel rational target for drug development against amebiasis.

The protealysin operon encodes emfourin, a prototype of a novel family of protein metalloprotease inhibitors

Protealysin is a Serratia proteamaculans metalloproteinase of the M4 peptidase family and the prototype of a large group of protealysin-like proteases (PLPs). PLPs are likely involved in bacterial interaction with plants and animals as well as in bacterial pathogenesis. We demonstrated that the PLP genes in bacteria colocalize with the genes of putative conserved proteins. In S. proteamaculans, these two genes form a bicistronic operon. The putative S. proteamaculans protein that we called emfourin (M4in) was expressed in Escherichia coli and characterized. M4in forms a complex with protealysin with a 1:1 stoichiometry and is a potent slow-binding competitive inhibitor of protealysin (K_i = 52 ± 14 pM); besides, M4in is not secreted from S. proteamaculans constitutively. A comparison of amino acid sequences of M4in and its homologs with those of known inhibitors suggests that M4in is the prototype of a new family of protein inhibitors of proteases.

Staphopains modulate Staphylococcus aureus biofilm integrity

Staphylococcus aureus is a known cause of chronic biofilm infections that can reside on medical implants or host tissue. Recent studies have demonstrated an important role for proteinaceous material in the biofilm structure. The S. aureus genome encodes many secreted proteases, and there is growing evidence that these enzymes have self-cleavage properties that alter biofilm integrity. However, the specific contribution of each protease and mechanism of biofilm modulation is not clear. To address this issue, we utilized a sigma factor B (ΔsigB) mutant where protease activity results in a biofilm-negative phenotype, thereby creating a condition where the protease(s) responsible for the phenotype could be identified. Using a plasma-coated microtiter assay, biofilm formation was restored to the ΔsigB mutant through the addition of the cysteine protease inhibitor E-64 or by using Staphostatin inhibitors that specifically target the extracellular cysteine proteases SspB and ScpA (called Staphopains). Through construction of gene deletion mutants, we determined that an sspB scpA double mutant restored ΔsigB biofilm formation, and this recovery could be replicated in plasma-coated flow cell biofilms. Staphopain levels were also found to be decreased under biofilm-forming conditions, possibly allowing biofilm establishment. The treatment of S. aureus biofilms with purified SspB or ScpA enzyme inhibited their formation, and ScpA was also able to disperse an established biofilm. The antibiofilm properties of ScpA were conserved across S. aureus strain lineages. These findings suggest an underappreciated role of the SspB and ScpA cysteine proteases in modulating S. aureus biofilm architecture.

Available methods for assembling expression cassettes for synthetic biology

Studies in the structural biology of the multicomponent protein complex, metabolic engineering, and synthetic biology frequently rely on the efficient over-expression of these subunits or enzymes in the same cell. As a first step, constructing the multiple expression cassettes will be a complicated and time-consuming job if the classic and conventional digestion and ligation based cloning method is used. Some more efficient methods have been developed, including (1) the employment of a multiple compatible plasmid expression system, (2) the rare-cutter-based design of vectors, (3) in vitro recombination (sequence and ligation independent cloning, the isothermally enzymatic assembly of DNA molecules in a single reaction), and (4) in vivo recombination using recombination-efficient yeast (in vivo assembly of overlapping fragments, reiterative recombination for the chromosome integration of foreign expression cassettes). In this review, we systematically introduce these available methods.

Papain-like proteases of Staphylococcus aureus

Staphylococcus aureus remains one of the major humanpathogens, causing a number of diverse infections. the growing antibiotic resistance, including vancomycin and methicilin-resistant strains raises the special interest in virulence mechanism of this pathogen. among a number of extracellular virulence factors, S. aureus secretes several proteases of three catalytic classes-metallo, serine and papain-like cysteine proteases. the expression of proteolytic enzymes is strictly controlled by global regulators of virulence factors expression agr and sar and proteases take a role in a phenotype change in postlogarithmic phase of growth. the staphylococcal proteases are secreted as proenzymes and undergo activation in a cascade manner. Staphopains, two cysteine, papain-like proteases of S. aureus are both approximately 20 kDa proteins that have almost identical three-dimensional structures, despite sharing limited primary sequence identity. although staphopain a displays activity similar to cathepsins, recognising hydrophobic residues at P2 position and large charged residues at P1, staphopain B differs significantly, showing significant preference towards β-branched residues at P2 and accepting only small, neutral residues at the P1 position. there is limited data available on the virulence potential of staphopains in in vivo models. However, in vitro experiments have demonstrated a very broad activity of these enzymes, including destruction of connective tissue, disturbance of clotting and kinin systems and direct interaction with host immune cells. Staphopain genes in various staphylococci species are regularly followed by a gene encoding an extremely specific inhibitor of the respective staphopain. This pattern is conserved across species and it is believed that inhibitors (staphostatins) protect the cytoplasm of the cell from premature activation of staphopains during protein folding. Notably, production and activity of staphopains is controlled on each level, from gene expression, through presence of specific inhibitors in cytoplasm, to the cascade-like activation in extracellular environment. Since these systems are highly conserved, this points to the importance of these proteases in the survival and/or pathogenicity of S. aureus.

α1-Antichymotrypsin inactivates staphylococcal cysteine protease in cross-class inhibition

Staphylococcal cysteine proteases are implicated as virulence factors in human and avian infections. Human strains of Staphylococcus aureus secrete two cysteine proteases (staphopains A and B), whereas avian strains express staphopain C (ScpA2), which is distinct from both human homologues. Here, we describe probable reasons why the horizontal transfer of a plasmid encoding staphopain C between avian and human strains has never been observed. The human plasma serine protease inhibitor α(1)-antichymotrypsin (ACHT) inhibits ScpA2. Together with the lack of ScpA2 inhibition by chicken plasma, these data may explain the exclusively avian occurrence of ScpA2. We also clarify the mechanistic details of this unusual cross-class inhibition. Analysis of mutated ACHT variants revealed that the cleavage of the Leu383-Ser384 peptide bond results in ScpA2 inhibition, whereas hydrolysis of the preceding peptide bond leads to ACHT inactivation. This evidence is consistent with the suicide-substrate-like mechanism of inhibition.

Prokaryote-derived protein inhibitors of peptidases: A sketchy occurrence and mostly unknown function

In metazoan organisms protein inhibitors of peptidases are important factors essential for regulation of proteolytic activity. In vertebrates genes encoding peptidase inhibitors constitute up to 1% of genes reflecting a need for tight and specific control of proteolysis especially in extracellular body fluids. In stark contrast unicellular organisms, both prokaryotic and eukaryotic consistently contain only few, if any, genes coding for putative peptidase inhibitors. This may seem perplexing in the light of the fact that these organisms produce large numbers of proteases of different catalytic classes with the genes constituting up to 6% of the total gene count with the average being about 3%. Apparently, however, a unicellular life-style is fully compatible with other mechanisms of regulation of proteolysis and does not require protein inhibitors to control their intracellular and extracellular proteolytic activity. So in prokaryotes occurrence of genes encoding different types of peptidase inhibitors is infrequent and often scattered among phylogenetically distinct orders or even phyla of microbiota. Genes encoding proteins homologous to alpha-2-macroglobulin (family I39), serine carboxypeptidase Y inhibitor (family I51), alpha-1-peptidase inhibitor (family I4) and ecotin (family I11) are the most frequently represented in Bacteria. Although several of these gene products were shown to possess inhibitory activity, with an exception of ecotin and staphostatins, the biological function of microbial inhibitors is unclear. In this review we present distribution of protein inhibitors from different families among prokaryotes, describe their mode of action and hypothesize on their role in microbial physiology and interactions with hosts and environment.

Functional assembly of a microbial consortium with autofluorescent and mineralizing activity for the biodegradation of organophosphates

Organophosphorus pesticides (OPs) cause serious environmental problems, and bioremediation using bacterial enzymes may provide an efficient and economical method for their detoxification. Green fluorescent protein (GFP) is a stable and easily detectable marker in monitoring genetically engineered microorganisms (GEMs) in the environment. In our research, the methyl parathion hydrolase gene (mpd) and enhanced green fluorescent protein gene (egfp) were successfully coexpressed using pETDuet vector in E. coli BL21 (DE3). The coexpression of methyl parathion hydrolase (MPH) and enhanced green fluorescent protein (EGFP) were confirmed by determining MPH activity and fluorescence intensity. The recombinant protein MPH showed high enzymatic degradative activity of several widely used OP residues on vegetables determined by GC analysis. Subsequently, a dual-species consortium comprising engineered E. coli and a natural p-nitrophenol (PNP) degrader Ochrobactrum sp. strain LL-1 for complete mineralization of dimethyl OPs was studied. It could completely mineralize methyl parathion (MP) via MP through PNP and hydroquinone and eventually through the TCA cycle as determined by HPLC analysis. The accumulation of PNP in suspended culture was prevented. The consortium could be further utilized for complete mineralization of PNP-substituted OPs in a laboratory-scale bioreactor and easily monitored by fluorescence of EGFP for its activity and fate.

Regulation of bacterial protease activity

Proteases, also referred to as peptidases, are the enzymes that catalyse the hydrolysis of peptide bonds in polipeptides. A variety of biological functions and processes depend on their activity. Regardless of the organism's complexity, peptidases are essential at every stage of life of every individual cell, since all protein molecules produced must be proteolytically processed and eventually recycled. Protease inhibitors play a crucial role in the required strict and multilevel control of the activity of proteases involved in processes conditioning both the physiological and pathophysiological functioning of an organism, as well as in host-pathogen interactions. This review describes the regulation of activity of bacterial proteases produced by dangerous human pathogens, focusing on the Staphylococcus genus.

The staphostatin family of cysteine protease inhibitors in the genus Staphylococcus as an example of parallel evolution of protease and inhibitor specificity

Staphostatins constitute a family of staphylococcal cysteine protease inhibitors sharing a lipocalin-like fold and a unique mechanism of action. Each of these cytoplasmic proteins is co-expressed from one operon, together with a corresponding target extracellular cysteine protease (staphopain). To cast more light on staphostatin/staphopain interaction and the evolution of the encoding operons, we have cloned and characterized a staphopain (StpA2aurCH-91) and its inhibitor (StpinA2aurCH-91) from a novel staphylococcal thiol protease operon (stpAB2CH-91) identified inS.aureusstrain CH-91. Furthermore, we have expressed a staphostatin fromStaphylococcus warneri(StpinBwar) and characterized its target protease (StpBwar). Analysis of the reciprocal interactions among novel and previously described members of the staphostatin and staphopain families demonstrates that the co-transcribed protease is the primary target for each staphostatin. Nevertheless, the inhibitor derived from one species ofStaphylococcuscan inhibit the staphopain from another species, although theKivalues are generally higher and inhibition only occurs if both proteins belong to the same subgroup of eitherS. aureusstaphopain A/staphostatin A (α group) or staphopain B/staphostatin B (β group) orthologs. This indicates that both subgroups arose in a single event of ancestral allelic duplication, followed by parallel evolution of the protease/inhibitor pairs. The tight coevolution is likely the result of the known deleterious effects of uncontrolled staphopain action.

Functional and structural characterization of Spl proteases from Staphylococcus aureus

Staphylococcus aureus is the major cause of nosocomial infections world-wide, with increasing prevalence of community-acquired diseases. The recent dramatic increase in multi-antibiotic resistance, including resistance to the last-resort drug, vancomycin, together with the lack of an effective vaccine highlight the need for better understanding of S.aureus pathogenicity. Comparative analysis of available bacterial genomes allows for the identification of previously uncharacterized S.aureus genes with potential roles in pathogenicity. A good example is a cluster of six serine protease-like (spl) genes encompassed in one operon, which encode for putative proteases with similarity to staphylococcal glutamylendopeptidase (V8 protease). Here, we describe an efficient expression system for the production of recombinant SplB and SplC proteases in Escherichia coli, together with structural and functional characterization of the purified enzymes. A unique mechanism of cytoplasm protection against activity of misdirected SplB was uncovered. Apparently, the co-translated signal peptide maintains protease latency until it is cleaved by the signal peptidase during protein secretion. Furthermore, the crystal structure of the SplC protease revealed a fold resembling that of the V8 protease and epidermolytic toxins. Arrangement of the active site cleft and substrate-binding pocket of SplC explains the mechanism of enzyme latency and suggests that some Spl proteases possess restricted substrate specificity similar to that of the V8 protease and epidermolytic toxins.

A novel endogenous inhibitor of the secreted streptococcal NAD-glycohydrolase

The Streptococcus pyogenes NAD-glycohydrolase (SPN) is a toxic enzyme that is introduced into infected host cells by the cytolysin-mediated translocation pathway. However, how S. pyogenes protects itself from the self-toxicity of SPN had been unknown. In this report, we describe immunity factor for SPN (IFS), a novel endogenous inhibitor that is essential for SPN expression. A small protein of 161 amino acids, IFS is localized in the bacterial cytoplasmic compartment. IFS forms a stable complex with SPN at a 1:1 molar ratio and inhibits SPN's NAD-glycohydrolase activity by acting as a competitive inhibitor of its β-NAD⁺ substrate. Mutational studies revealed that the gene for IFS is essential for viability in those S. pyogenes strains that express an NAD-glycohydrolase activity. However, numerous strains contain a truncated allele of ifs that is linked to an NAD-glycohydrolase−deficient variant allele of spn. Of practical concern, IFS allowed the normally toxic SPN to be produced in the heterologous host Escherichia coli to facilitate its purification. To our knowledge, IFS is the first molecularly characterized endogenous inhibitor of a bacterial β-NAD⁺−consuming toxin and may contribute protective functions in the streptococci to afford SPN-mediated pathogenesis.

The gram-positive bacterium Streptococcus pyogenes is a human pathogen that causes a wide range of infections from pharyngitis (“strep throat”) to invasive necrotizing fasciitis (“flesh-eating disease”). While strep throat responds to antibiotic therapy, more invasive infections caused by S. pyogenes often require surgical intervention. It is currently unknown exactly how the bacteria can switch between the different types of infection, but one possibility is via a mechanism by which the bacterium injects a bacterial protein toxin (S. pyogenes NAD-glycohydrolase [SPN]) into human skin cells, causing their death. In this study, the authors have shown that the injected toxin also has the ability to affect the bacteria. A second protein neutralizes SPN to ensure the bacteria are immune to its toxic effects. Consequently, S. pyogenes has developed a valuable weapon in its arsenal to promote its survival by ensuring the safe production of SPN, through its own protection by immunity factor for SPN, enabling the delivery of active SPN into human cells. The process reported in this paper may ultimately help create therapeutic inhibitors of SPN and possibly other SPN-like toxins implicated in microbial disease progression.

A comparison of staphostatin B with standard mechanism serine protease inhibitors

Staphostatins are the endogenous, highly specific inhibitors of staphopains, the major secreted cysteine proteases from Staphylococcus aureus. We have previously shown that staphostatins A and B are competitive, active site-directed inhibitors that span the active site clefts of their target proteases in the same orientation as substrates. We now report the crystal structure of staphostatin B in complex with wild-type staphopain B at 1.9 A resolution. In the complex structure, the catalytic residues are found in exactly the positions that would be expected for uncomplexed papain-type proteases. There is robust, continuous density for the staphostatin B binding loop and no indication for cleavage of the peptide bond that comes closest to the active site cysteine of staphopain B. The carbonyl carbon atom C of this peptide bond is 4.1 A away from the active site cysteine sulfur Sgamma atom. The carbonyl oxygen atom O of this peptide bond points away from the putative oxyanion hole and lies almost on a line from the Sgamma atom to the C atom. The arrangement is strikingly similar to the "ionmolecule" arrangement for the complex of papain-type enzymes with their substrates but differs significantly from the arrangement conventionally assumed for the Michaelis complex of papain-type enzymes with their substrates and also from the arrangement that is crystallographically observed for complexes of standard mechanism inhibitors and their target serine proteases.