On the functional interchangeability, oxidant versus reductant, of members of the thioredoxin superfamily

Can thiol-based redox systems be utilized as parts for synthetic biology applications?

OBJECTIVES

Synthetic biology has emerged from molecular biology and engineering approaches and aims to develop novel, biologically-inspired systems for industrial and basic research applications ranging from biocomputing to drug production. Surprisingly, redoxin (thioredoxin, glutaredoxin, peroxiredoxin) and other thiol-based redox systems have not been widely utilized in many of these synthetic biology applications.

METHODS

We reviewed thiol-based redox systems and the development of synthetic biology applications that have used thiol-dependent parts.

RESULTS

The development of circuits to facilitate cytoplasmic disulfide bonding, biocomputing and the treatment of intestinal bowel disease are amongst the applications that have used thiol-based parts. We propose that genetically encoded redox sensors, thiol-based biomaterials and intracellular hydrogen peroxide generators may also be valuable components for synthetic biology applications.

DISCUSSION

Thiol-based systems play multiple roles in cellular redox metabolism, antioxidant defense and signaling and could therefore offer a vast and diverse portfolio of components, parts and devices for synthetic biology applications. However, factors limiting the adoption of redoxin systems for synthetic biology applications include the orthogonality of thiol-based components, limitations in the methods to characterize thiol-based systems and an incomplete understanding of the design principles of these systems.

Release of redox enzymes and micro-RNAs in extracellular vesicles, during infection and inflammation

Many studies reported that redox enzymes, particularly thioredoxin and peroxiredoxin, can be released by cells and act as soluble mediators in immunity. Recently, it became clear that peroxiredoxins can be secreted via the exosome-release route, yet it remains unclear how this exactly happens and why. This review will first introduce briefly the possible redox states of protein cysteines and the role of redox enzymes in their regulation. We will then discuss the studies on the extracellular forms of some of these enzymes, their association with exosomes/extracellular vesicles and with exosome micro-RNAs (miRNAs)/mRNAs involved in oxidative processes, relevant in infection and inflammation.

Structural insight into the biological functions of Arabidopsis thaliana ACHT1

The Arabidopsis thaliana atypical Cys His-rich thioredoxins (ACHTs) are a small class of atypical thioredoxins (TRXs) located in chloroplasts thylakoids and are characterized by a noncanonical motif at their redox active site, C (G/S)(S/G)C. Previous studies have reported that ACHT1 can interact with A. thaliana 2-Cys peroxiredoxins (2-Cys Prxs, including PrxA and PrxB) to transmit oxidation signals in response to illumination with normal light intensity. In this study, we reported the crystal structure of ACHT1 and show that ACHT1 adopts a canonical TRX fold. Comparison of the structures of ACHT1 in both reducing and oxidizing environments revealed that while the redox environment did not influence the overall structure of ACHT1, it did change the conformation of its catalytic residues. We found that the catalytic C125 of ACHT1 is the target residue for PrxA in vitro. In addition, we found that ACHT1 can reduce the peroxidase activity of PrxA, and further confirmed that the ability of ACHT1 to restore the peroxidase function of PrxA was due to the interaction between the two. Our results provide a structural basis for studying the function of atypical TRXs and the oxidative regulation mechanism of ACHT1 and 2-Cys Prxs in chloroplasts.

Identification and functional characterization of thioredoxin-related protein of 14 kDa in Oncomelania hupensis, the intermediate host of Schistosoma japonicum

Oncomelania hupensis is the unique intermediate host of the blood fluke Schistosoma japonicum, which causes schistosomiasis. In snails, highly toxic reactive oxygen species (ROS) can be continually generated by hemocytes in response to foreign particles or pathogens, and may be involved in damaging and eliminating digenean larvae. Thioredoxin-related protein of 14 kDa (TRP14) is a member of the Trx superfamily, and plays an important role in the scavenging of ROS. This study was designed to identify and characterize TRP14 from O. hupensis (OhTRP14), and investigate the involvement of OhTRP14 in the scavenging of ROS in snail host immune response to the parasite S. japonicum. Here we expressed and purified the recombinant OhTRP14 and its mutant, and rOhTRP14 displayed oxidoreductase activity dependent on the CPDC motif. OhTRP14 protein was ubiquitously present in all the tested snail tissues, and especially immunolocalized in the cytoplasm of immune cell types (hemocytes). Both the expression of OhTRP14 and ROS level increased significantly in snails following challenge with S. japonicum. The dsRNA-mediated knockdown of OhTRP14 was successfully conducted by oral feeding, and ROS production was increased by OhTRP14 knockdown, implying that OhTRP14 was involved in the scavenging of ROS in O. hupensis circulating hemocytes. Therefore, we conclude that OhTRP14 may be involved in the scavenging of ROS in snail host immune response to the parasite S. japonicum. The results expand our understanding of the interaction between this parasite and host, and lay a foundation for the establishment of Oncomelania-schistosome infection models.

Disulfide bond formation in prokaryotes

Interest in protein disulfide bond formation has recently increased because of the prominent role of disulfide bonds in bacterial virulence and survival. The first discovered pathway that introduces disulfide bonds into cell envelope proteins consists of Escherichia coli enzymes DsbA and DsbB. Since its discovery, variations on the DsbAB pathway have been found in bacteria and archaea, probably reflecting specific requirements for survival in their ecological niches. One variation found amongst Actinobacteria and Cyanobacteria is the replacement of DsbB by a homologue of human vitamin K epoxide reductase. Many Gram-positive bacteria express enzymes involved in disulfide bond formation that are similar, but non-homologous, to DsbAB. While bacterial pathways promote disulfide bond formation in the bacterial cell envelope, some archaeal extremophiles express proteins with disulfide bonds both in the cytoplasm and in the extra-cytoplasmic space, possibly to stabilize proteins in the face of extreme conditions, such as growth at high temperatures. Here, we summarize the diversity of disulfide-bond-catalysing systems across prokaryotic lineages, discuss examples for understanding the biological basis of such systems, and present perspectives on how such systems are enabling advances in biomedical engineering and drug development.

A role for 2-Cys peroxiredoxins in facilitating cytosolic protein thiol oxidation

Hydrogen peroxide (H₂O₂) acts as a signaling messenger by triggering the reversible oxidation of redox-regulated proteins. It remains unclear how proteins can be oxidized by signaling levels of H₂O₂ in the presence of peroxiredoxins, which are highly efficient peroxide scavengers. Here we show that the rapid formation of disulfide bonds in cytosolic proteins is enabled, rather than competed, by cytosolic 2-Cys peroxiredoxins. Under the conditions tested, the combined deletion or depletion of cytosolic peroxiredoxins broadly frustrated H₂O₂-dependent protein thiol oxidation, which is the exact opposite of what would be predicted based on the assumption that H₂O₂ oxidizes proteins directly. We find that peroxiredoxins enable rapid and sensitive protein thiol oxidation by relaying H₂O₂-derived oxidizing equivalents to other proteins. Although these findings do not rule out the existence of Prx-independent H₂O₂ signaling mechanisms, they suggest a broader role for peroxiredoxins as sensors and transmitters of H₂O₂ signals than hitherto recognized.

Engineering of Helicobacter pylori Dimeric Oxidoreductase DsbK (HP0231)

The formation of disulfide bonds that are catalyzed by proteins of the Dsb (disulfide bond) family is crucial for the correct folding of many extracytoplasmic proteins. Thus, this formation plays an essential, pivotal role in the assembly of many virulence factors. The Helicobacter pylori disulfide bond-forming system is uncomplicated compared to the best-characterized Escherichia coli Dsb pathways. It possesses only two extracytoplasmic Dsb proteins named HP0377 and HP0231. As previously shown, HP0377 is a reductase involved in the process of cytochrome c maturation. Additionally, it also possesses disulfide isomerase activity. HP0231 was the first periplasmic dimeric oxidoreductase involved in disulfide generation to be described. Although HP0231 function is critical for oxidative protein folding, its structure resembles that of dimeric EcDsbG, which does not confer this activity. However, the HP0231 catalytic motifs (CXXC and the so-called cis-Pro loop) are identical to that of monomeric EcDsbA. To understand the functioning of HP0231, we decided to study the relations between its sequence, structure and activity through an extensive analysis of various HP0231 point mutants, using in vivo and in vitro strategies. Our work shows the crucial role of the cis-Pro loop, as changing valine to threonine in this motif completely abolishes the protein function in vivo. Functioning of HP0231 is conditioned by the combination of CXXC and the cis-Pro loop, as replacing the HP0231 CXXC motif by the motif from EcDsbG or EcDsbC results in bifunctional protein, at least in E. coli. We also showed that the dimerization domain of HP0231 ensures contact with its substrates. Moreover, the activity of this oxidase is independent on the structure of the catalytic domain. Finally, we showed that HP0231 chaperone activity is independent of its redox function.

Insights into Trx1, TRP14, and Prx1 homologs of Paralichthys olivaceus: molecular profiles and transcriptional responses to immune stimulations

Thioredoxin (Trx) proteins are involved in several cellular processes, such as anti-oxidative stress and cellular redox homeostasis. In this study, we isolated the full-length cDNAs of PoTrx1 and PoTRP14 from Japanese flounder (Paralichthys olivaceus). PoTrx1 is 723 bp in length, with a 366-bp open reading frame (ORF) that encodes for 121 amino acids. PoTRP14 is 909 bp in length, with a 372-bp ORF that encodes for 123 amino acids. PoTrx1 and PoTRP14 are highly conserved in Cys-Gly-Pro-Cys and Cys-Pro-Asp-Cys forms, respectively. Tissue distribution analysis revealed that the transcripts of PoTrx1 and PoTRP14 were ubiquitously expressed in all tested tissues and particularly abundant in immunity-related organs, such as the liver, intestine, gill, and spleen. Development expression profiles indicated that PoTrx1 transcript was expressed from the neurula stage to the 1 day post-hatching stage; the maximum transcript levels were recorded at the somatic stage. The mRNA level of PoTRP14 was constantly expressed at all examined developmental stages, reaching the peak at the before-hatching stage. Prx1 is a peroxiredoxin family member that serves similar functions to PoTrx1 and PoTRP14. A primary hepatocyte culture system was established to examine the immunoregulatory properties of PoTrx1, PoTRP14, and Prx1 in response to lipopolysaccharide, CuSO4, and H2O2 stimulation. Results revealed that the transcript levels of PoTrx1, PoTRP14, and Prx1 were significantly up-regulated in a time-dependent manner after the immunostimulant challenge. These data suggest that PoTrx1, PoTRP14, and Prx1 play critical roles in anti-oxidation and immunoregulation.

Disulfide bond formation in prokaryotes: history, diversity and design

The formation of structural disulfide bonds is essential for the function and stability of a great number of proteins, particularly those that are secreted. There exists a variety of dedicated cellular catalysts and pathways from archaea to humans that ensure the formation of native disulfide bonds. In this review we describe the initial discoveries of these pathways and report progress in recent years in our understanding of the diversity of these pathways in prokaryotes, including those newly discovered in some archaea. We will also discuss the various successful efforts to achieve laboratory-based evolution and design of synthetic disulfide bond formation machineries in the bacterium Escherichia coli. These latter studies have also led to new more general insights into the redox environment of the cytoplasm and bacterial cell envelope. This article is part of a Special Issue entitled: Thiol-Based Redox Processes.

Identification and characterization of TRP14, a thioredoxin-related protein of 14 kDa from orange-spotted grouper, Epinephelus coioides

Thioredoxin (abbreviated as Trx) is an important ubiquitous disulfide reductase, which can protect organisms against various oxidative stresses. In the present study, a thioredoxin-related protein of 14 kDa (named as Ec-TRP14) was identified from the marine fish grouper, Epinephelus coioides by RACE PCR. The full-length cDNA of Ec-TRP14 was comprised of 1066 bp with a 372 bp open reading frame that encodes a putative protein of 123 amino acids. Similar to most TRP14s, Ec-TRP14 contained the conserved motif C-P-D-C. Ec-TRP14 mRNA is predominately expressed in liver, brain and muscle. The expression of Ec-TRP14 was up-regulated in the liver of grouper challenged with SGIV. Ec-TRP14 was recombined and expressed in Escherichia coli BL21 (DE3), and the rEc-Ec-TRP14 fusion protein was demonstrated to possess the antioxidant activity. The grouper spleen (GS) cells were treated with a high concentration of rEc-TRP14 (8.3 μg/ml), which significantly enhanced cells viability under damage caused by viral infection. These results together indicated that Ec-TRP14 could function as an important antioxidant in a physiological context, and might be involved in the responses to viral challenge.

Effect of posttranslational modifications on enzyme function and assembly

The detailed examination of enzyme molecules by mass spectrometry and other techniques continues to identify hundreds of distinct PTMs. Recently, global analyses of enzymes using methods of contemporary proteomics revealed widespread distribution of PTMs on many key enzymes distributed in all cellular compartments. Critically, patterns of multiple enzymatic and nonenzymatic PTMs within a single enzyme are now functionally evaluated providing a holistic picture of a macromolecule interacting with low molecular mass compounds, some of them being substrates, enzyme regulators, or activated precursors for enzymatic and nonenzymatic PTMs. Multiple PTMs within a single enzyme molecule and their mutual interplays are critical for the regulation of catalytic activity. Full understanding of this regulation will require detailed structural investigation of enzymes, their structural analogs, and their complexes. Further, proteomics is now integrated with molecular genetics, transcriptomics, and other areas leading to systems biology strategies. These allow the functional interrogation of complex enzymatic networks in their natural environment. In the future, one might envisage the use of robust high throughput analytical techniques that will be able to detect multiple PTMs on a global scale of individual proteomes from a number of carefully selected cells and cellular compartments. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.

Protein folding drives disulfide formation

PDI catalyzes the oxidative folding of disulfide-containing proteins. However, the sequence of reactions leading to a natively folded and oxidized protein remains unknown. Here we demonstrate a technique that enables independent measurements of disulfide formation and protein folding. We find that non-native disulfides are formed early in the folding pathway and can trigger misfolding. In contrast, a PDI domain favors native disulfides by catalyzing oxidation at a late stage of folding. We propose a model for cotranslational oxidative folding wherein PDI acts as a placeholder that is relieved by the pairing of cysteines caused by substrate folding. This general mechanism can explain how PDI catalyzes oxidative folding in a variety of structurally unrelated substrates.

The biological roles of glutaredoxins

Grxs (glutaredoxins) are small ubiquitous redox enzymes. They are generally involved in the reduction of oxidative modifications using glutathione. Grxs are not only able to reduce protein disulfides and the low-molecular-mass antioxidant dehydroascorbate, but also represent the major enzyme class responsible for deglutathionylation reactions. Functional proteomics, including interaction studies, comparative activity measurements using heterologous proteins and structural analysis are combined to provide important insights into the crucial function of Grxs in cellular redox networks. Summarizing the current understanding of Grxs, with a special focus on organelle-localized members across species, genus and kingdom boundaries (including cyanobacteria, plants, bacteria, yeast and humans) lead to two different classifications, one according to sequence structure that gives insights into the diversification of Grxs, and another according to function within the cell that provides a basis for assessing the different roles of Grxs.

Isolation and characterization of a thioredoxin domain-containing protein 12 from orange-spotted grouper, Epinephelus coioides

Thioredoxin domain-containing protein 12 (Txndc12) belongs to the thioredoxin superfamily, and has roles in redox regulation, defense against oxidative stress, refolding of disulfide-containing proteins, and regulation of transcription factors. In this study, a thioredoxin domain-containing protein 12 was cloned from the marine fish grouper, Epinephelus coioides by RACE PCR, named as Ec-Txndc12. The Ec-Txndc12 encodes 173 amino acid residues with signal peptide in its N-terminal and a thioredoxin (Trx) domain that is homologous with some genes in Mus musculus, Xenopus laveis, etc. Ec-Txndc12 mRNA is predominately expressed in liver, brain and muscle. The expression of Ec-Txndc12 was up-regulated in the liver of grouper challenged with SGIV. In order to elucidate its biological functions, Ec-Txndc12 was recombined and expressed in Escherichia coli BL21 (DE3). The rEc-Txndc12 fusion protein was demonstrated to possess the antioxidant activity. The grouper spleen (GS) cells were treated with a high concentration of rEc-Txndc12 (30 μg/ml), which significantly enhanced cells viability under oxidative damage caused by viral infection. These results together indicated that Ec-Txndc12 could function as an important antioxidant in a physiological context, and might be involved in the responses to viral challenge.

Media composition: antioxidants/chelators and cellular function

Protection of embryos against oxidative insults during culture is necessary to maintain viability. Generation of excessive levels of reactive oxygen species (ROS) is triggered by various components of the in vitro environment, most of which embryos do not normally encounter in vivo. To compensate for these deficiencies in the culture environment, antioxidants and chelators are often used to control or suppress ROS levels as embryos develop. However, there is no consensus regarding dosage, time of exposure, or appropriate combinations of antioxidants and chelators in embryo culture. In order to elucidate this aspect of an embryo's chemical surroundings in vitro, we present the current knowledge on the function and effect of each antioxidant or chelator that is often included in an embryo culture medium.

Mechanisms of oxidative protein folding in the bacterial cell envelope

Disulfide-bond formation is important for the correct folding of a great number of proteins that are exported to the cell envelope of bacteria. Bacterial cells have evolved elaborate systems to promote the joining of two cysteines to form a disulfide bond and to repair misoxidized proteins. In the past two decades, significant advances have occurred in our understanding of the enzyme systems (DsbA, DsbB, DsbC, DsbG, and DsbD) used by the gram-negative bacterium Escherichia coli to ensure that correct pairs of cysteines are joined during the process of protein folding. However, a number of fundamental questions about these processes remain, especially about how they occur inside the cell. In addition, recent recognition of the increasing diversity among bacteria in the disulfide bond-forming capacity and in the systems for introducing disulfide bonds into proteins is raising new questions. We review here the marked progress in this field and discuss important questions that remain for future studies.

Fluorescent protein-based redox probes

Redox biochemistry is increasingly recognized as an integral component of cellular signal processing and cell fate decision making. Unfortunately, our capabilities to observe and measure clearly defined redox processes in the natural context of living cells, tissues, or organisms are woefully limited. The most advanced and promising tools for specific, quantitative, dynamic and compartment-specific observations are genetically encoded redox probes derived from green fluorescent protein (GFP). Within only few years from their initial introduction, redox-sensitive yellow FP (rxYFP), redox-sensitive GFPs (roGFPs), and HyPer have generated enormous interest in applying these novel tools to monitor dynamic redox changes in vivo. As genetically encoded probes, these biosensors can be specifically targeted to different subcellular locations. A critical advantage of roGFPs and HyPer is their ratiometric fluorogenic behavior. Moreover, the probe scaffold of redox-sensitive fluorescent proteins (rxYFP and roGFPs) is amenable to molecular engineering, offering fascinating prospects for further developments. In particular, the engineering of redox relays between roGFPs and redox enzymes allows control of probe specificity and enhancement of sensitivity. Genetically encoded redox probes enable the functional analysis of individual proteins in cellular redox homeostasis. In addition, redox biosensor transgenic model organisms offer extended opportunities for dynamic in vivo imaging of redox processes.

A small family of chloroplast atypical thioredoxins

The reduction and the formation of regulatory disulfide bonds serve as a key signaling element in chloroplasts. Members of the thioredoxin (Trx) superfamily of oxidoreductases play a major role in these processes. We have characterized a small family of plant-specific Trxs in Arabidopsis (Arabidopsis thaliana) that are rich in cysteine and histidine residues and are typified by a variable noncanonical redox active site. We found that the redox midpoint potential of three selected family members is significantly less reducing than that of the classic Trxs. Assays of subcellular localization demonstrated that all proteins are localized to the chloroplast. Selected members showed high activity, contingent on a dithiol electron donor, toward the chloroplast 2-cysteine peroxiredoxin A and poor activity toward the chloroplast NADP-malate dehydrogenase. The expression profile of the family members suggests that they have distinct roles. The intermediate redox midpoint potential value of the atypical Trxs might imply adaptability to function in modulating the redox state of chloroplast proteins with regulatory disulfides.

Functional plasticity of a peroxidase allows evolution of diverse disulfide-reducing pathways

In Escherichia coli, the glutathione/glutaredoxin and thioredoxin pathways are essential for the reduction of cytoplasmic protein disulfide bonds, including those formed in the essential enzyme ribonucleotide reductase during its action on substrates. Double mutants lacking thioredoxin reductase (trxB) and glutathione reductase (gor) or glutathione biosynthesis (gshA) cannot grow. Growth of Deltagor DeltatrxB strains is restored by a mutant (ahpC*) of the peroxiredoxin AhpC, converting it to a disulfide reductase that generates reduced glutathione. Here, we show that ahpC* also restores growth to a DeltagshB DeltatrxB strain, which lacks glutathione and accumulates only its precursor gamma-glutamylcysteine (gamma-GC). It suppresses this strain by allowing accumulation of reduced gamma-GC, which can substitute for glutathione. Surprisingly, new ahpC suppressor mutations arose in a DeltagshA DeltatrxB strain lacking both glutathione and gamma-GC, a strain that ahpC* does not suppress. Some of these mutant AhpC proteins channel electrons into the disulfide-reducing pathways via either the thioredoxins or the glutaredoxins without, evidently, the intermediary of glutathione. Our results provide insights into the physiological functioning of the glutathione pathway and reveal surprising plasticity of a peroxidase because different mutant versions of AhpC can channel electrons into the disulfide-reducing pathways by at least four distinct routes. Despite the reductase activity of mutant AhpCs, these various suppressor strains exhibit an oxidizing cytoplasm and accumulate correctly folded disulfide-bonded proteins in their cytoplasm. Proteins most effectively oxidized vary between strains, potentially providing useful tools for expressing different disulfide-bonded proteins.

Thioredoxins and glutaredoxins as facilitators of protein folding

Thiol-disulfide oxidoreductase systems of bacterial cytoplasm and eukaryotic cytosol favor reducing conditions and protein thiol groups, while bacterial periplasm and eukaryotic endoplasmatic reticulum provide oxidizing conditions and a machinery for disulfide bond formation in the secretory pathway. Oxidoreductases of the thioredoxin fold superfamily catalyze steps in oxidative protein folding via protein-protein interactions and covalent catalysis to act as chaperones and isomerases of disulfides to generate a native fold. The active site dithiol/disulfide of thioredoxin fold proteins is CXXC where variations of the residues inside the disulfide ring are known to increase the redox potential like in protein disulfide isomerases. In the catalytic mechanism thioredoxin fold proteins bind to target proteins through conserved backbone-backbone hydrogen bonds and induce conformational changes of the target disulfide followed by nucleophilic attack by the N-terminally located low pK(a) Cys residue. This generates a mixed disulfide covalent bond which subsequently is resolved by attack from the C-terminally located Cys residue. This review will focus on two members of the thioredoxin superfamily of proteins known to be crucial for maintaining a reduced intracellular redox state, thioredoxin and glutaredoxin, and their potential functions as facilitators and regulators of protein folding and chaperone activity.

Glutathionylation pathways in drug response

Regulation of protein function through post-translational modifications (PTM) can be important pharmacological target, and there are drugs developed to modulate specific PTM such as protein kinase or histone deacetylase inhibitors. We are still far behind in considering protein glutathionylation as pharmacological target as the biological consequences and role of this PTM are still unclear. We discuss the possible relevance of glutathionylation in diseases and its biases compared with other PTM. In particular, we discuss the different roles of glutathionylation in the context of redox regulation as opposed to that of oxidative stress, and the difficulties arising from the overlaps of these two concepts.

Role of reversible, thioredoxin-sensitive oxidative protein modifications in cardiac myocytes

Reactive oxygen species (ROS) are important mediators of myocardial remodeling. However, the precise molecular mechanisms by which ROS exert their effects are incompletely understood. ROS induce oxidative posttranslational protein modifications that can regulate the function of structural, functional, and signaling proteins. For example, oxidative modification of free reactive thiols (S-thiolation) on the small G protein Ras increases Ras activity and thereby promotes ROS-dependent hypertrophic signaling in cardiac myocytes. By reducing thiols and restoring reversible thiol modifications, thioredoxin and glutaredoxin can act as regulators of ROS-mediated protein function. Understanding the regulation and functional relevance of oxidative protein modifications in myocardial remodeling may lead to new therapeutic strategies.

The crystal structure of yeast protein disulfide isomerase suggests cooperativity between its active sites

Protein disulfide isomerase plays a key role in catalyzing the folding of secretory proteins. It features two catalytically inactive thioredoxin domains inserted between two catalytically active thioredoxin domains and an acidic C-terminal tail. The crystal structure of yeast PDI reveals that the four thioredoxin domains are arranged in the shape of a twisted "U" with the active sites facing each other across the long sides of the "U." The inside surface of the "U" is enriched in hydrophobic residues, thereby facilitating interactions with misfolded proteins. The domain arrangement, active site location, and surface features strikingly resemble the Escherichia coli DsbC and DsbG protein disulfide isomerases. Biochemical studies demonstrate that all domains of PDI, including the C-terminal tail, are required for full catalytic activity. The structure defines a framework for rationalizing the differences between the two active sites and their respective roles in catalyzing the formation and rearrangement of disulfide bonds.

A selection for mutants that interfere with folding of Escherichia coli thioredoxin-1 in vivo

Escherichia coli thioredoxin is normally a cytoplasmic protein involved in the reduction of disulfide bonds. However, thioredoxin can be translocated to the periplasm when it is attached to a cotranslational signal sequence. When exported to the periplasm, it can partially replace the activity of DsbA in promoting the formation of disulfide bonds. In contrast, when thioredoxin is fused to a posttranslational signal sequence, very little of it appears in the periplasm. We propose that this absence of posttranslational export is due to the rapid folding of thioredoxin in the cytoplasm. We sought mutants of thioredoxin that retarded its folding in the cytoplasm, which we accomplished by fusing thioredoxin to a posttranslational signal sequence and selecting for mutants in which thioredoxin was exported to the periplasm, where it could replace DsbA. The collection of mutants obtained represents a limited number of amino acid changes in the protein. In vitro studies on purified mutant proteins show that all but one are defective in the kinetics and thermodynamics of protein folding. We propose that the slower folding of the thioredoxin mutant proteins in the cytoplasm allows their export by a posttranslational pathway. We discuss some implications of this class of mutants for aspects of the folding pathway of thioredoxin and for its mechanism of export. In particular, the finding that a folding mutant that allows protein translocation alters an amino acid at the C terminus of the protein suggests that the degree to which thioredoxin folds during its translation must be severely restricted.

Conserved role of the linker alpha-helix of the bacterial disulfide isomerase DsbC in the avoidance of misoxidation by DsbB

In the bacterial periplasm the co-existence of a catalyst of disulfide bond formation (DsbA) that is maintained in an oxidized state and of a reduced enzyme that catalyzes the rearrangement of mispaired cysteine residues (DsbC) is important for the folding of proteins containing multiple disulfide bonds. The kinetic partitioning of the DsbA/DsbB and DsbC/DsbD pathways partly depends on the ability of DsbB to oxidize DsbA at rates >1000 times greater than DsbC. We show that the resistance of DsbC to oxidation by DsbB is abolished by deletions of one or more amino acids within the alpha-helix that connects the N-terminal dimerization domain with the C-terminal thioredoxin domain. As a result, mutant DsbC carrying alpha-helix deletions could catalyze disulfide bond formation and complemented the phenotypes of dsbA cells. Examination of DsbC homologues from Haemophilus influenzae, Pseudomonas aeruginosa, Erwinia chrysanthemi, Yersinia pseudotuberculosis, Vibrio cholerae (30-70% sequence identity with the Escherichia coli enzyme) revealed that the mechanism responsible for avoiding oxidation by DsbB is a general property of DsbC family enzymes. In addition we found that deletions in the linker region reduced, but did not abolish, the ability of DsbC to assist the formation of active vtPA and phytase in vivo, in a DsbD-dependent manner, revealing that interactions between DsbD and DsbC are also conserved.

Regulation of protein function by glutathionylation

The main function of reduced glutathione (GSH) is to protect from oxidative stress as a reactive oxygen scavenger. However, in the context of redox regulation, the ratio between GSH and its oxidized form (GSSG) determines the redox state of redox-sensitive cysteines in some proteins and, thus, acts as a signaling system. While GSH/GSSG can catalyze oxido-reduction of intra- and inter-chain disulfides by thiol-disulfide exchange, this review focuses on the formation of mixed disulfides between glutathione and proteins, also known as glutathionylation. The review discusses the regulatory role of this post-translational modification and the role of protein disulfide oxidoreductases (thioredoxin/thioredoxin reductase, glutaredoxin, protein disulfide isomerase) in the reversibility of this process.

Use of thioredoxin as a reporter to identify a subset of Escherichia coli signal sequences that promote signal recognition particle-dependent translocation

We have previously reported that the DsbA signal sequence promotes efficient, cotranslational translocation of the cytoplasmic protein thioredoxin-1 via the bacterial signal recognition particle (SRP) pathway. However, two commonly used signal sequences, those of PhoA and MalE, which promote export by a posttranslational mechanism, do not export thioredoxin. We proposed that this difference in efficiency of export was due to the rapid folding of thioredoxin in the cytoplasm; cotranslational export by the DsbA signal sequence avoids the problem of cytoplasmic folding (C. F. Schierle, M. Berkmen, D. Huber, C. Kumamoto, D. Boyd, and J. Beckwith, J. Bacteriol. 185:5706-5713, 2003). Here, we use thioredoxin as a reporter to distinguish SRP-dependent from non-SRP-dependent cleavable signal sequences. We screened signal sequences exhibiting a range of hydrophobicity values based on a method that estimates hydrophobicity. Successive iterations of screening and refining the method defined a threshold hydrophobicity required for SRP recognition. While all of the SRP-dependent signal sequences identified were above this threshold, there were also a few signal sequences above the threshold that did not utilize the SRP pathway. These results suggest that a simple measure of the hydrophobicity of a signal sequence is an important but not a sufficient indicator for SRP recognition. In addition, by fusing a number of both classes of signal sequences to DsbA, we found that DsbA utilizes an SRP-dependent signal sequence to achieve efficient export to the periplasm. Our results suggest that those proteins found to be exported by SRP-dependent signal sequences may require this mode of export because of their tendency to fold rapidly in the cytoplasm.

Prediction of pKa and redox properties in the thioredoxin superfamily

Electrostatic interactions play important roles in diverse biological phenomena controlling the function of many proteins. Polar molecules can be studied with the FDPB method solving the Poisson-Boltzmann equation on a finite difference grid. A method for the prediction of pK(a)s and redox potentials in the thioredoxin superfamily is introduced. The results are compared with experimental pK(a) data where available, and predictions are made for members lacking such data. Studying CxxC motif variation in the context of different background structures permits analysis of contributions to cysteine DeltapK(a)s. The motif itself and the overall framework regulate pK(a) variation. The reported method includes generation of multiple side-chain rotamers for the CxxC motif and is an effective predictive tool for functional pK(a) variation across the superfamily. Redox potential follows the trend in cysteine pK(a) variation, but some residual discrepancy indicates that a pH-independent factor plays a role in determining redox potentials for at least some members of the superfamily. A possible molecular basis for this feature is discussed.

Isolation and characterization of a novel human thioredoxin-like gene hTLP19 encoding a secretory protein

A novel human gene, named as hTLP19, was isolated and characterized as secretory protein by combining bioinformatics tools with experiments. The hTLP19 encodes 172 amino acid residues with signal peptide in its N-terminal and a thioredoxin (Trx) domain that is homologous with some genes in Mus musculus, Xenopus laevis, etc. Moreover, the result from insulin reduction assay indicated that the hTLP19 protein has Trx enzymatic activity. By comparing full-length cDNA with human genomic DNA, the hTLP19 gene might have seven coding exons spanning 35 kb of genomic DNA on the human chromosome 1p32.3. Northern blot analysis showed that human hTLP19 is expressed widely in many tissues with 1.6 kb band and extra 1.2 kb band in placenta. Subcellular localization and immunoblotting assays indicated that hTLP19 might be secreted out of cell through trans-Golgi network (TGN).

Protein disulfide bond formation in prokaryotes

Disulfide bonds formed between pairs of cysteines are important features of the structure of many proteins. Elaborate electron transfer pathways have evolved Escherichia coli to promote the formation of these covalent bonds and to ensure that the correct pairs of cysteines are joined in the final folded protein. These transfers of electrons consist, in the main, of cascades of disulfide bond formation or reduction steps between a series of proteins (DsbA, DsbB, DsbC, and DsbD). A surprising variety of mechanisms and protein structures are involved in carrying out these steps.

The DsbA signal sequence directs efficient, cotranslational export of passenger proteins to the Escherichia coli periplasm via the signal recognition particle pathway

The Escherichia coli cytoplasmic protein thioredoxin 1 can be efficiently exported to the periplasmic space by the signal sequence of the DsbA protein (DsbAss) but not by the signal sequence of alkaline phosphatase (PhoA) or maltose binding protein (MBP). Using mutations of the signal recognition particle (SRP) pathway, we found that DsbAss directs thioredoxin 1 to the SRP export pathway. When DsbAss is fused to MBP, MBP also is directed to the SRP pathway. We show directly that the DsbAss-promoted export of MBP is largely cotranslational, in contrast to the mode of MBP export when the native signal sequence is utilized. However, both the export of thioredoxin 1 by DsbAss and the export of DsbA itself are quite sensitive to even the slight inhibition of SecA. These results suggest that SecA may be essential for both the slow posttranslational pathway and the SRP-dependent cotranslational pathway. Finally, probably because of its rapid folding in the cytoplasm, thioredoxin provides, along with gene fusion approaches, a sensitive assay system for signal sequences that utilize the SRP pathway.

Functions of thiol-disulfide oxidoreductases in E. coli: redox myths, realities, and practicalities

A large family of enzymes contributes to the thiol-disulfide redox environment of the cells of most organisms. These proteins belong to pathways that carry out a variety of reactions, including the promotion of disulfide bond formation in extracytoplasmic proteins, the isomerization of proteins with incorrect disulfide bonds, and the reduction of disulfide bonds in the active sites of cytoplasmic proteins. Although the redox activities of these proteins measured in vitro often is consistent with the role (oxidant or reductant) these proteins perform in vivo, this is not always the case. The measured redox potentials can even suggest a function for a protein opposite of that which it carries out in the cell. Structural features of such proteins can contribute to a direction of electron transfer inconsistent with the redox potential. Furthermore, the environment in which such proteins are found may determine the protein's physiological role. Detailed analysis of these proteins in Escherichia coli provides strains that are useful for biotechnological purposes. Increasing the activity of certain of these proteins in the cell envelope or altering the thiol-disulfide redox environment of the cytoplasm to make it more oxidizing enhances the yield of useful disulfide bond-containing proteins such as tissue plasminogen activator and immunoglobulins.

Mechanism of the electron transfer catalyst DsbB from Escherichia coli

The membrane protein DsbB from Escherichia coli is essential for disulfide bond formation and catalyses the oxidation of the periplasmic dithiol oxidase DsbA by ubiquinone. DsbB contains two catalytic disulfide bonds, Cys41-Cys44 and Cys104-Cys130. We show that DsbB directly oxidizes one molar equivalent of DsbA in the absence of ubiquinone via disulfide exchange with the 104-130 disulfide bond, with a rate constant of 2.7 x 10 M(-1) x s(-1). This reaction occurs although the 104-130 disulfide is less oxidizing than the catalytic disulfide bond of DsbA (E(o)' = -186 and -122 mV, respectively). This is because the 41-44 disulfide, which is only accessible to ubiquinone but not to DsbA, is the most oxidizing disulfide bond in a protein described so far, with a redox potential of -69 mV. Rapid intramolecular disulfide exchange in partially reduced DsbB converts the enzyme into a state in which Cys41 and Cys44 are reduced and thus accessible for reoxidation by ubiquinone. This demonstrates that the high catalytic efficiency of DsbB results from the extreme intrinsic oxidative force of the enzyme.

Cathepsin B responsiveness to glutathione and lipoic acid redox

Some subcomponents of cell protein degradation exhibit an unexplained reductive energy requirement; and diverse cysteine proteases are among multiple effector mechanisms requiring reduction. Present studies investigated whether cathepsin B activity is graded in response to (a) reduced glutathione (GSH) and dihydrolipoic acid (DHLA) concentrations, (b) their redox ratios, and (c) their differential potencies and efficacies. Purified bovine cathepsin B activity was assayed with carbobenzyloxy-Arg-Arg-aminomethylcoumarin by standard methods following inactivation by spontaneous air oxidation. Endogenous GSH concentration (2-3 mM) maintained 30-40% of the maximal cathepsin B reaction rate observed under dithiothreitol (5 mM). Following activation with GSH, the cathepsin B reaction rate was inhibited in proportion to nonphysiologic GSH:GSSG redox ratio above 1% oxidized (e.g., 85% inhibited at 3 mM:2 mM). Thus, cathepsin B can be redox buffered by the GSH:GSSG ratio. DHLA was identified as a potent cathepsin activator with threshold near 1 microM and 80% maximal activation near 10 microM. Conversely, oxidized lipoamide disulfide inhibited cathepsin B over 5-250 microM. DHLA at 5-50 microM superimposed severalfold additional activation upon the stable submaximal cathepsin B reaction rate maintained by endogenous GSH concentration (2-3 mM). Cell protein degradation was bioassayed by release of [3H] leucine from the biosynthetically labeled rat heart under nonrecirculating perfusion. The pro-oxidant, diamide (100 microM), reversibly inhibited 80% of basal proteolysis. Supraphysiologic extracellular DHLA (80 microM) doubled the basal rate of averaged cell protein degradation in 15 min. Thus, the cell redox system buffers an intermediate rate of protein degradation, which can be decreased by supraphysiologic exposure to diamide pro-oxidant or increased by DHLA reductant.

Roles of thiol-redox pathways in bacteria

Disulfide bonds in proteins play various important roles. They are either formed as structural features to stabilize the protein or are found only transiently as part of a catalytic or regulatory cycle. In vivo, the formation and reduction of disulfide bonds is catalyzed by specialized thiol-disulfide exchanging enzymes that contain an active site with the sequence motif Cys-X-X-Cys. These proteins have structurally evolved to catalyze predominantly either oxidative reactions or reductive steps. There is mounting evidence that, in addition to the thiol redox potential, the spatial distribution within different cell compartments and the overall redox state of the cell are equally important. In the cytoplasm, multiple pathways play overlapping roles in the reduction of disulfide bonds and additionally, the expression of several components of thiol-redox pathways was shown to respond to the changes in the cellular thiol-redox equilibrium. In the periplasm, two systems coexist, one catalyzing thiol oxidation and the other disulfide reduction. Recent results suggest that two different mechanisms are used to translocate reducing power from the cytoplasm or to dissipate the electrons after oxidation.

Turning a disulfide isomerase into an oxidase: DsbC mutants that imitate DsbA

There are two distinct pathways for disulfide formation in prokaryotes. The DsbA-DsbB pathway introduces disulfide bonds de novo, while the DsbC-DsbD pathway functions to isomerize disulfides. One of the key questions in disulfide biology is how the isomerase pathway is kept separate from the oxidase pathway in vivo. Cross-talk between these two systems would be mutually destructive. To force communication between these two systems we have selected dsbC mutants that complement a dsbA null mutation. In these mutants, DsbC is present as a monomer as compared with dimeric wild-type DsbC. Based on these findings we rationally designed DsbC mutants in the dimerization domain. All of these mutants are able to rescue the dsbA null phenotype. Rescue depends on the presence of DsbB, the native re-oxidant of DsbA, both in vivo and in vitro. Our results suggest that dimerization acts to protect DsbC's active sites from DsbB-mediated oxidation. These results explain how oxidative and reductive pathways can co-exist in the periplasm of Escherichia coli.

Effect of sequences of the active-site dipeptides of DsbA and DsbC on in vivo folding of multidisulfide proteins in Escherichia coli

We have examined the role of the active-site CXXC central dipeptides of DsbA and DsbC in disulfide bond formation and isomerization in the Escherichia coli periplasm. DsbA active-site mutants with a wide range of redox potentials were expressed either from the trc promoter on a multicopy plasmid or from the endogenous dsbA promoter by integration of the respective alleles into the bacterial chromosome. The dsbA alleles gave significant differences in the yield of active murine urokinase, a protein containing 12 disulfides, including some that significantly enhanced urokinase expression over that allowed by wild-type DsbA. No direct correlation between the in vitro redox potential of dsbA variants and the urokinase yield was observed. These results suggest that the active-site CXXC motif of DsbA can play an important role in determining the folding of multidisulfide proteins, in a way that is independent from DsbA's redox potential. However, under aerobic conditions, there was no significant difference among the DsbA mutants with respect to phenotypes depending on the oxidation of proteins with few disulfide bonds. The effect of active-site mutations in the CXXC motif of DsbC on disulfide isomerization in vivo was also examined. A library of DsbC expression plasmids with the active-site dipeptide randomized was screened for mutants that have increased disulfide isomerization activity. A number of DsbC mutants that showed enhanced expression of a variant of human tissue plasminogen activator as well as mouse urokinase were obtained. These DsbC mutants overwhelmingly contained an aromatic residue at the C-terminal position of the dipeptide, whereas the N-terminal residue was more diverse. Collectively, these data indicate that the active sites of the soluble thiol- disulfide oxidoreductases can be modulated to enhance disulfide isomerization and protein folding in the bacterial periplasmic space.

Periplasmic transit and disulfide bond formation of the autotransported Shigella protein IcsA

The Shigella outer membrane protein IcsA belongs to the family of type V secreted (autotransported) virulence factors. Members of this family mediate their own translocation across the bacterial outer membrane: the carboxy-terminal beta domain forms a beta barrel channel in the outer membrane through which the amino-terminal alpha domain passes. IcsA, which is localized at one pole of the bacterium, mediates actin assembly by Shigella, which is essential for bacterial intracellular movement and intercellular dissemination. Here, we characterize the transit of IcsA across the periplasm during its secretion. We show that an insertion in the dsbB gene, whose gene product mediates disulfide bond formation of many periplasmic intermediates, does not affect the surface expression or unipolar targeting of IcsA. However, IcsA forms one disulfide bond in the periplasm in a DsbA/DsbB-dependent fashion. Furthermore, cellular fractionation studies reveal that IcsA has a transient soluble periplasmic intermediate. Our data also suggest that IcsA is folded in a proteinase K-resistant state in the periplasm. From these data, we propose a novel model for the secretion of IcsA that may be applicable to other autotransported proteins.

Transmembrane electron transfer by the membrane protein DsbD occurs via a disulfide bond cascade

The cytoplasmic membrane protein DsbD transfers electrons from the cytoplasm to the periplasm of E. coli, where its reducing power is used to maintain cysteines in certain proteins in the reduced state. We split DsbD into three structural domains, each containing two essential cysteines. Remarkably, when coexpressed, these truncated proteins restore DsbD function. Utilizing this three piece system, we were able to determine a pathway of the electrons through DsbD. Our findings strongly suggest that the pathway is based on a series of multistep redox reactions that include direct interactions between thioredoxin and DsbD, and between DsbD and its periplasmic substrates. A thioredoxin-fold domain in DsbD appears to have the novel role of intramolecular electron shuttle.

Roles of a conserved arginine residue of DsbB in linking protein disulfide-bond-formation pathway to the respiratory chain of Escherichia coli

The active-site cysteines of DsbA, the periplasmic disulfide-bond-forming enzyme of Escherichia coli, are kept oxidized by the cytoplasmic membrane protein DsbB. DsbB, in turn, is oxidized by two kinds of quinones (ubiquinone for aerobic and menaquinone for anaerobic growth) in the electron-transport chain. We describe the isolation of dsbB missense mutations that change a highly conserved arginine residue at position 48 to histidine or cysteine. In these mutants, DsbB functions reasonably well aerobically but poorly anaerobically. Consistent with this conditional phenotype, purified R48H exhibits very low activity with menaquinone and an apparent Michaelis constant (K(m)) for ubiquinone seven times greater than that of the wild-type DsbB, while keeping an apparent K(m) for DsbA similar to that of wild-type enzyme. From these results, we propose that this highly conserved arginine residue of DsbB plays an important role in the catalysis of disulfide bond formation through its role in the interaction of DsbB with quinones.

Redox properties of protein disulfide bond in oxidized thioredoxin and lysozyme: a pulse radiolysis study

We have studied the one-electron reduction of oxidized Chlamydomonas reinhardtii thioredoxin and compared it to that of hen egg white lysozyme, using CO(2)(*) (-) free radicals as reductants. This comparison shows that the thioredoxin disulfide/thiol redox couple has different properties than that of lysozyme: the disulfide radical pK(a) is much lower (around 5 for small disulfides, 4.62 for lysozyme, <3 for thioredoxin). To get a better understanding of the modulation of the thioredoxin redox properties we have constructed the mutants W35A and D30A. Their reduction by pulse radiolysis indicates that W35 strongly controls both the disulfide radical acidity (the pK(a) in W35A is equal to ca. 4), and the thiol reactivity. Asp30 is also involved in the control of proton transfer to the disulfide free radical. In addition, its removal seems to increase the reduction potential of the thioredoxin thiyl/thiol couple. Overall, the reduction properties of thioredoxin confirm its nature as a unique reductant.

A thioredoxin from the hyperthermophilic archaeon Methanococcus jannaschii has a glutaredoxin-like fold but thioredoxin-like activities

A thioredoxin homologue (Mj0307) from the hyperthermophilic archaeon Methanococcus jannaschii (MjTRX) was cloned, produced in E. coli, and compared to the thioredoxin from E. coli (ETRX). The secondary structure profile of MjTRX obtained by NMR spectroscopy shows that it has four beta-sheets and three alpha-helices arranged in betaalphabetaalphabetabetaalpha, similar to that of glutaredoxin. However, MjTRX supports the growth of T7 bacteriophage in E. coli and is weakly reduced by the thioredoxin reductase from E. coli, indicating that MjTRX is functionally closer to a thioredoxin than a glutaredoxin. MjTRX has higher specific insulin reductase activity than ETRX and retained its full activity over 4 days at 95 degrees C, whereas ETRX lost its activity in 150 min. The standard state redox potential of MjTRX is about -277 mV, which is the lowest value thus far known among redox potentials of the thioredoxin superfamily. This indicates that the lower redox potential is necessary in keeping catalytic disulfide bonds reduced in the cytoplasm and in coping with oxidative stress in an anaerobic hyperthermophile.