An in vivo method for characterization of protein interactions within sulfur trafficking systems of E. coli

Sulfur trafficking systems are multiprotein systems that synthesize sulfur-containing cofactors such as iron-sulfur clusters. The sulfur is derived enzymatically from cysteine and transferred between nucleophilic cysteine residues within proteins until incorporation into the relevant cofactor. As these systems are poorly understood, we have developed an in vivo method for characterizing these interactions and have applied our method to the SUF system of Escherichia coli, which is responsible for iron-sulfur cluster biogenesis under oxidative stress and iron limitation. Proteins that interact covalently with SufE were trapped in vivo, purified, and identified by mass spectrometry. We identified SufE-SufS and SufE-SufB interactions, interactions previously demonstrated in vitro, indicating that our method has the ability to identify physiologically relevant interactions. The sulfur acceptor function of SufE is likely due to the low pK(a) of its active site C51, which we determined to be 6.3 ± 0.7. We found that SufE interacts with several Fe-S cluster proteins, further supporting the validity of the method, and with tryptophanase, glutaredoxin-3, and glutaredoxin-4, possibly suggesting a role for these enzymes in iron-sulfur biogenesis by the SUF system. Our results indicate that this method could serve as a general tool for the determination of sulfur trafficking mechanisms.

Proteomic analysis of protein-protein interactions within the Cysteine Sulfinate Desulfinase Fe-S cluster biogenesis system

Fe-S cluster biogenesis is of interest to many fields, including bioenergetics and gene regulation. The CSD system is one of three Fe-S cluster biogenesis systems in E. coli and is comprised of the cysteine desulfurase CsdA, the sulfur acceptor protein CsdE, and the E1-like protein CsdL. The biological role, biochemical mechanism, and protein targets of the system remain uncharacterized. Here we present that the active site CsdE C61 has a lowered pK(a) value of 6.5, which is nearly identical to that of C51 in the homologous SufE protein and which is likely critical for its function. We observed that CsdE forms disulfide bonds with multiple proteins and identified the proteins that copurify with CsdE. The identification of Fe-S proteins and both putative and established Fe-S cluster assembly (ErpA, glutaredoxin-3, glutaredoxin-4) and sulfur trafficking (CsdL, YchN) proteins supports the two-pathway model, in which the CSD system is hypothesized to synthesize both Fe-S clusters and other sulfur-containing cofactors. We suggest that the identified Fe-S cluster assembly proteins may be the scaffold and/or shuttle proteins for the CSD system. By comparison with previous analysis of SufE, we demonstrate that there is some overlap in the CsdE and SufE interactomes.

The role of active site residues in the oxidant specificity of the Orp1 thiol peroxidase

In this study we investigated the role of active site residues in the peroxidase activity of Orp1 (GPx3) using three different peroxide substrates. Using a structural homology model of the reduced form of Orp1, we identified Asn126 and Phe127 as evolutionarily conserved residues that line the back of the Orp1 active site and which are likely to affect the peroxidase activity of Orp1. Additionally, we identified Phe38 as a surface residue that could influence substrate specificity as it is located adjacent to Cys36, in the same position occupied by similar hydrophobic amino acids in many Orp1 homologs. We individually mutated these residues to alanine and examined the effect of each mutation in vitro and in vivo. Chloro-4-nitrobenzo-2-oxa-1,3-diazole was used to identify Cys-SOH modification of Cys36 in response to H(2)O(2), tert-butyl-hydroperoxide (tert-BHP), and cumene hydroperoxide (CHP) in Orp1(WT). Mutation of Asn126 and Phe127 eliminate Cys-SOH formation and peroxidase activity in response to H(2)O(2), tert-BHP and CHP. Furthermore, the pK(a) of Cys36 is elevated closer to that of free cysteine compared to Orp1(WT). Mutation of Phe38 does not affect the peroxidase activity of Orp1 upon exposure to H(2)O(2). The Phe38 mutation decreases Orp1 peroxidase activities in response to either tert-BHP or CHP. The in vivo sensitivity of the Phe38 mutant to both tert-BHP and CHP is increased, while the H(2)O(2) sensitivity is unchanged. The pK(a) of Cys36 in the Phe38 mutant is 5.0, which is the same as Orp1(WT). Taken together, these results suggest that Phe38 does not play a role in the reactivity of Cys36, but does modulate the affinity of Orp1 for alkyl hydroperoxides.

Formation, reactivity, and detection of protein sulfenic acids

It has become clear in recent decades that the post-translational modification of protein cysteine residues is a crucial regulatory event in biology. Evidence supports the reversible oxidation of cysteine thiol groups as a mechanism of redox-based signal transduction, while the accumulation of proteins with irreversible thiol oxidations is a hallmark of stress-induced cellular damage. The initial formation of cysteine-sulfenic acid (SOH) derivatives, along with the reactive properties of this functional group, serves as a crossroads whereby the local redox environment may dictate the progression of either regulatory or pathological outcomes. Protein-SOH are established as transient intermediates in the formation of more stable cysteine oxidation products both under basal conditions and in response to several redox-active extrinsic compounds. This review details both direct and multistep chemical routes proposed to generate protein-SOH, the spectrum of secondary reactions that may follow their initial formation and the arsenal of experimental tools available for their detection. Pioneering studies that have provided a framework for our current understanding of protein-SOH as well as state-of-the-art proteomic strategies designed for global assessments of this post-translational modification are highlighted.

Context-dependent effects of parental effort on malaria infection in a wild bird population, and their role in reproductive trade-offs

Although trade-offs between reproductive effort and other fitness components are frequently documented in wild populations, the underlying physiological mechanisms remain poorly understood. Parasitism has been suggested to mediate reproductive trade-offs, yet only a limited number of parasite taxa have been studied, and reproductive effort-induced changes in parasitism are rarely linked to trade-offs observed in the same population. We conducted a brood size manipulation experiment in blue tits (Cyanistes caeruleus) infected with malaria (Plasmodium) parasites, and used quantitative PCR to measure changes in parasitaemia. In one of two years investigated, parasitaemia increased as a result of brood enlargement, and was also positively associated with two other indicators of reproductive effort: clutch size and single parenthood. These associations between both experimental and naturally varying reproductive effort and parasitaemia suggest that immune control of chronic malaria infections can be compromised when parents are working hard. Brood size manipulation significantly affected the number of independent offspring produced, which was maximised when brood size was unchanged. Moreover, when parents were infected with one of two common Plasmodium species, the shape of this trade-off curve was more pronounced, suggesting that parasitic infection may exacerbate the trade-off between quantity and quality of offspring. Although the involvement of parasites in survival costs of reproduction has received much attention, these results suggest their role in other commonly documented reproductive trade-offs, such as that between number and quality of offspring, warrants further study.

Seasonal variation in Plasmodium prevalence in a population of blue tits Cyanistes caeruleus

1. Seasonal variation in environmental conditions is ubiquitous and can affect the spread of infectious diseases. Understanding seasonal patterns of disease incidence can help to identify mechanisms, such as the demography of hosts and vectors, which influence parasite transmission dynamics. 2. We examined seasonal variation in Plasmodium infection in a blue tit Cyanistes caeruleus population over 3 years using sensitive molecular diagnostic techniques, in light of Beaudoin et al.'s (1971; Journal of Wildlife Diseases, 7, 5-13) model of seasonal variation in avian malaria prevalence in temperate areas. This model predicts a within-year bimodal pattern of spring and autumn peaks with a winter absence of infection. 3. Avian malaria infections were mostly Plasmodium (24.4%) with occasional Haemoproteus infections (0.8%). Statistical nonlinear smoothing techniques applied to longitudinal presence/absence data revealed marked temporal variation in Plasmodium prevalence, which apparently showed a within-year bimodal pattern similar to Beaudoin et al.'s model. However, of the two Plasmodium morphospecies accounting for most infections, only the seasonal pattern of Plasmodium circumflexum supported Beaudoin et al.'s model. On closer examination there was also considerable age structure in infection: Beaudoin et al.'s seasonal pattern was observed only in first year and not older birds. Plasmodium relictum prevalence was less seasonally variable. 4. For these two Plasmodium morphospecies, we reject Beaudoin et al.'s model as it does not survive closer scrutiny of the complexities of seasonal variation among Plasmodium morphospecies and host age classes. Studies of host-parasite interactions should consider seasonal variation whenever possible. We discuss the ecological and evolutionary implications of seasonal variation in disease prevalence.

A genetically encoded probe for cysteine sulfenic acid protein modification in vivo

All organisms have defense mechanisms to combat the deleterious effects of oxidative damage produced by reactive oxidative species (ROS). Although it is known that ROS play a major role in oxidative damage, increasing evidence reveals that ROS have wider cellular effects through their role in many signal transduction pathways. Here we have adapted a redox-regulated domain from the Yap1 transcription factor in Saccharomyces cerevisiae to function as a general trap for proteins that form cysteine sulfenic acid (Cys-SOH) in vivo. In response to H2O2, the Yap1 probe forms mixed disulfide bonds with a variety of proteins. The formation of these protein complexes is time dependent and peroxide concentration dependent. Disulfide-bonded complex formation can be attenuated by the addition of dimedone, a compound that specifically reacts with Cys-SOH, indicating the specificity of the probe toward Cys-SOH. An efficient one-step purification procedure was developed for proteins trapped by the Yap1 probe, and the constituents were identified by mass spectrometry. This methodology identified six proteins in Escherichia coli that contain redox-active cysteine residues known to form Cys-SOH as part of their catalytic cycle. The results suggest that the Yap1 probe is useful for identifying Cys-SOH-regulated proteins and can be employed in any genetically tractable organism to monitor transient Cys-SOH formation in vivo.

Molecular mechanism of oxidative stress perception by the Orp1 protein

In this study we investigated the molecular mechanism by which the Orp1 (Gpx3) protein in Saccharomyces cerevisiae senses and reacts with hydrogen peroxide. Upon exposure to H(2)O(2) Orp1(Cys36) forms a disulfide-bonded complex with the C-terminal domain of the Yap1 protein (Yap1-cCRD). We used 4-nitrobenzo-2-oxa-1,3-diazole to identify a cysteine sulfenic acid (Cys-SOH) modification that forms on Cys(36) of Orp1(Cys36) upon exposure to H(2)O(2). Under similar conditions, neither Cys(82) of Orp1(Cys82) nor Cys(598) of Yap1 forms Cys-SOH. A homology-based molecular model of Orp1 suggests that the structure of the active site of Orp1 is similar to that found in mammalian selenocysteine glutathione peroxidases. Proposed active site residues Gln(70) and Trp(125) form a catalytic triad with Cys(36) in the Orp1 molecular model. The remainder of the active site pocket is formed by Phe(38), Asn(126), and Phe(127), which are evolutionarily conserved residues. We made Q70A and W125A mutants and tested the ability of these mutants to form Cys-SOH in response to H(2)O(2). Both mutants were unable to form Cys-SOH and did not form a H(2)O(2)-inducible disulfide-bonded complex with Yap1-cCRD. The pK(a) of Cys(36) was determined to be 5.1, which is 3.2 pH units lower than that of a free cysteine (8.3). In contrast, Orp1 Cys(82) (the resolving cysteine) has a pK(a) value of 8.3. The pK(a) of Cys(36) in the Q70A and W125A mutants is also 8.3, demonstrating the importance of these residues in modulating the nucleophilic character of Cys(36). Finally, we show that S. cerevisiae strains with ORP1 Q70A and W125A mutations are less tolerant to H(2)O(2) than those containing wild-type ORP1. The results of our study suggest that attempts to identify novel redox-regulated proteins and signal transduction pathways should focus on characterization of low pK(a) cysteines.

Within-population variation in prevalence and lineage distribution of avian malaria in blue tits,Cyanistes caeruleus

The development of molecular genetic screening techniques for avian blood parasites has revealed many novel aspects of their ecology, including greatly elevated diversity and complex host-parasite relationships. Many previous studies of malaria in birds have treated single study populations as spatially homogeneous with respect to the likelihood of transmission of malaria to hosts, and we have very little idea whether any spatial heterogeneity influences different malaria lineages similarly. Here, we report an analysis of variation in the prevalence and cytochrome b lineage distribution of avian malaria infection with respect to environmental and host factors, and their interactions, in a single blue tit (Cyanistes caeruleus) population. Of 11 Plasmodium and Haemoproteus cytochrome b lineages found in 997 breeding individuals, the three most numerous (pSGS1, pTURDUS1 and pBT7) were considered separately, in addition to analyses of all avian malaria lineages pooled. Our analyses revealed marked spatial differences in the prevalence and distribution of these lineages, with local prevalence of malaria within the population ranging from over 60% to less than 10%. In addition, we found several more complex patterns of prevalence with respect to local landscape features, host state, parasite genotype, and their interactions. We discuss the implications of such heterogeneity in parasite infection at a local scale for the study of the ecology and evolution of infectious diseases in natural populations. The increased resolution afforded by the combination of molecular genetic and geographical information systems (GIS) tools has the potential to provide many insights into the epidemiology, evolution and ecology of these parasites in the future.

Parasites entangled in food webs

Food webs are a fundamental concept in ecology in which parasites have been virtually ignored. In a recent article, Lafferty et al. address this imbalance, finding that the inclusion of parasites in food webs could be of greater importance to ecosystem stability than was previously thought. Furthermore, the bottom of the food chain is perhaps no longer the most dangerous place to be.

Thermodynamic Basis for Redox Regulation of the Yap1 Signal Transduction Pathway

The Yap1 oxidative stress signal transduction pathway found in Saccharomyces cerevisiae is redox-regulated. We have examined the thermodynamic basis of the disulfide/dithiol couples that are involved in the regulation of this pathway. The oxidized form of the Yap1 redox domain (Yap1-RD) fragment, derived from the Yap1 transcription factor, contains two disulfide bonds, one between Cys303 and Cys598 and one between Cys310 and Cys629. Oxidation-reduction titrations reveal the presence of two separate two-electron redox couples in Yap1-RD, with redox midpoint potentials (E(m)) of -155 and -330 mV, respectively, at pH 7.0. We measured E(m) values of -275 and -265 mV for the two cytoplasmic S. cerevisiae thioredoxins, Trx1 and Trx2, respectively, both at pH 7.0. Last, we measured an E(m) value of -255 mV for the Cys36-Cys82 disulfide bond at pH 6.0 in the glutathione peroxidase-like enzyme, oxidant receptor protein (Orp1). We were unable to obtain satisfactory redox titration data for Orp1 at pH 7.0, but if the redox-active disulfide of Orp1 exhibits the -59 mV per pH unit dependence for E(m) typical of protein disulfides in this pH region, an E(m) value of -315 mV can be estimated for Orp1 at pH 7.0 by extrapolation. Together, these data suggest that, at physiological ratios of Trx(ox)/Trx(red), the reduction of both the E(m) = -315 mV disulfide of Orp1 and the E(m) = -330 mV disulfide of Yap1 by either Trx1 or Trx2 would be thermodynamically possible.

Mutational analysis to define an activating region on the redox-sensitive transcriptional regulator OxyR

The OxyR transcription factor is a key regulator of the Escherichia coli response to oxidative stress. Previous studies showed that OxyR binding to a target promoter enhances RNA polymerase binding and vice versa, suggesting a direct interaction between OxyR and RNA polymerase. To identify the region of OxyR that might contact RNA polymerase, we carried out alanine scanning and random mutagenesis of oxyR. The combination of these approaches led to the identification of several mutants defective in the activation of an OxyR target gene. A subset of the mutations map to the DNA-binding domain, other mutations appear to affect dimerization of the regulatory domain, while another group is suggested to affect disulfide bond formation. The two mutations, D142A and R273H, giving the most dramatic phenotype are located in a patch on the surface of the oxidized OxyR protein and possibly define an activating region on OxyR.

Protein secondary structure prediction with dihedral angles

We present DESTRUCT, a new method of protein secondary structure prediction, which achieves a three-state accuracy (Q3) of 79.4% in a cross-validated trial on a nonredundant set of 513 proteins. An iterative set of cascade-correlation neural networks is used to predict both secondary structure and psi dihedral angles, with predicted values enhancing the subsequent iteration. Predictive accuracies of 80.7% and 81.7% are achieved on the CASP4 and CASP5 targets, respectively. Our approach is significantly more accurate than other contemporary methods, due to feedback and a novel combination of structural representations.

The hitchhiker's guide to avian malaria

The ecological mechanisms underlying the dispersal of parasites are poorly understood, which is of particular concern in view of currently emerging infectious diseases. In a new study, Pérez-Tris and Bensch examined the distribution and prevalence of avian malaria in a migratory bird across Western Europe. They concluded that repeated independent evolution of year-round transmission has enabled some avian malaria lineages to become more widespread, and more prevalent, than lineages that are transmitted only during the summer. This study blurs the boundaries of evolutionary ecology, epidemiology and macroecology with great potential for cross-disciplinary research.

Structural and functional consequences of methionine oxidation in thrombomodulin

Thrombomodulin (TM) is an endothelial cell surface glycoprotein that is responsible for switching the catalytic activity of thrombin away from fibrinogen cleavage (pro-coagulant) and towards protein C cleavage (anticoagulant). Although TM is a large protein, only the fourth and fifth epidermal growth factor-like (EGF-like) domains are required for anticoagulant function. These two domains must work together, and the linker between the two domains contains a single methionine residue, Met 388. Oxidation of Met 388 is deleterious for TM activity. Structural studies, both X-ray and NMR, of wild type and variants at position 388 show that Met 388 provides a key linkage between the two domains. Oxidation of the methionine has consequences for the structure of the fifth domain, which binds to thrombin. Oxidation also appears to disrupt the interdomain contacts resulting in structural and dynamic changes. The functional consequences of oxidation of Met 388 include decreased anticoagulant activity. Oxidative stress from several causes is reflected in lower serum levels of activated protein C and a higher thrombotic tendency, and this is thought to be linked to the oxidation of Met 388 in TM. Thus, TM structure and function are altered in a subtle but functionally critical way upon oxidation of Met 388.

Learned kin recognition cues in a social bird

In many cooperatively breeding birds, kin selection has an important role in the evolution and maintenance of social behaviour, and 'helpers' can maximize indirect fitness gains by preferentially allocating care to close relatives. Although there is evidence for kin-biased helping behaviour in several species, the mechanism of kin recognition underlying this behaviour is poorly understood. Vocalizations are the most commonly used cues in avian recognition systems, but the effectiveness of vocal signals as reliable recognition cues must depend on how they are acquired. However, there have been no experimental studies of the development of vocal recognition cues in cooperative birds; indeed, the ontogeny of all bird vocalizations other than song is poorly known in any species. Here, we show that cooperatively breeding long-tailed tits (Aegithalos caudatus) can discriminate between kin and non-kin according to the individual-specific characteristics of contact calls, and show experimentally that individuals learn these calls from provisioning adults during the nestling period. Finally, we show that the pattern of cooperative behaviour in this species is consistent with the use of recognition cues learned through association.

Dynamics of the fragment of thrombomodulin containing the fourth and fifth epidermal growth factor-like domains correlate with function

Thrombomodulin (TM) forms a 1:1 complex with thrombin. Whereas thrombin alone cleaves fibrinogen to make the fibrin clot, the thrombin-TM complex cleaves protein C to initiate the anticoagulant pathway. The fourth and fifth EGF-like domains of TM together form the minimal fragment with anticoagulant cofactor activity. A short linker connects the fourth and fifth EGF-like domains of TM, and Met 388 in the middle of the linker interacts with both domains. Several different structures of TMEGF45 variants are now available, and these show that mutation of Met 388 alters the structure of the fifth domain, as well as the connectivity of the two domains. To probe this phenomenon more thoroughly, NMR backbone dynamics experiments have been carried out on the individual fourth and fifth domains as well as on the wild type, the Met 388 Leu mutant, and the variant in which Met 388 is oxidized. The results presented here show that changes at Met 388 cause significant changes in backbone dynamics in both the fourth and fifth EGF-like domains of TM. Backbone dynamics within the small loop of the fourth domain Tyr 358 correlate with anticoagulant cofactor activity. Backbone dynamics of the thrombin-binding residues Tyr 413 and Ile 414 are inversely correlated with thrombin binding. The preordering of the backbone of Tyr 413 and Ile 414 only occurs in the two-domain fragments, revealing a role for the fourth domain in thrombin binding as well as in anticoagulant cofactor activity.

CSF spectrophotometry in the diagnosis and exclusion of spontaneous subarachnoid haemorrhage

AIMS

To assess the sensitivity and specificity of CSF spectrophotometry for the detection of xanthochromia in patients with clinical symptoms suggestive of subarachnoid haemorrhage (SAH) but normal cranial computed tomography (CT).

METHODS

All consecutive patients undergoing both cranial CT and lumbar puncture for investigation of possible SAH at the Princess Alexandra Hospital, Brisbane, between January 2000 and April 2003 were included in the study. All case histories, radiology and laboratory results were retrospectively assessed. The sensitivity, specificity and positive predictive value of the spectrophotometry test were calculated.

RESULTS

253 patients were included in the study. Spectrophotometry was shown to have a sensitivity of 100% but a specificity of only 75.2%. The positive predictive value of spectrophotometry as an indicator of SAH was 3.3%.

CONCLUSIONS

CSF spectrophotometry has an unacceptably low specificity and positive predictive value, which greatly limit its use as a clinical tool.

Stabilizing natural selection on the early expression of a secondary sexual trait in a passerine bird

Natural selection is a central tenet of evolutionary theory, yet the estimation of the direction and intensity of selection remains problematic. Here, we assess the strength of selection on the early expression of a secondary sexual ornament, bill colour, in male European blackbirds (Turdus merula) using 5 years of capture-mark-recapture (CMR) data. The best-fitting model consisted of a quadratic relationship between survival rate and bill colour, indicating stabilizing natural selection on the early expression of a secondary sexual trait. There was no evidence for sexual selection acting on bill colour in the first year. We suggest that the consideration of early selection and the adoption of refined statistical methods may reveal patterns of selection in the wild that have, as yet, remained undetected.

Structural basis for redox regulation of Yap1 transcription factor localization

The ability of organisms to alter their gene expression patterns in response to environmental changes is essential for viability. A central regulator of the response to oxidative stress in Saccharomyces cerevisiae is the Yap1 transcription factor. Upon activation by increased levels of reactive oxygen species, Yap1 rapidly redistributes to the nucleus where it regulates the expression of up to 70 genes. Here we identify a redox-regulated domain of Yap1 and determine its high-resolution solution structure. In the active oxidized form, a nuclear export signal (NES) in the carboxy-terminal cysteine-rich domain is masked by disulphide-bond-mediated interactions with a conserved amino-terminal alpha-helix. Point mutations that weaken the hydrophobic interactions between the N-terminal alpha-helix and the C-terminal NES-containing domain abolished redox-regulated changes in subcellular localization of Yap1. Upon reduction of the disulphide bonds, Yap1 undergoes a change to an unstructured conformation that exposes the NES and allows redistribution to the cytoplasm. These results reveal the structural basis of redox-dependent Yap1 localization and provide a previously unknown mechanism of transcription factor regulation by reversible intramolecular disulphide bond formation.

Predicting protein secondary structure by cascade-correlation neural networks

The back-propagation neural network algorithm is a commonly used method for predicting the secondary structure of proteins. Whilst popular, this method can be slow to learn and here we compare it with an alternative: the cascade-correlation architecture. Using a constructive algorithm, cascade-correlation achieves predictive accuracies comparable to those obtained by back-propagation, in shorter time.

NMR structures reveal how oxidation inactivates thrombomodulin

Oxidation of Met 388, one of the three linker residues connecting the fourth and fifth EGF-like domains of thrombomodulin (TM), is deleterious for TM activity. An NMR structure of the smallest active fragment of TM (TMEGF45) and a crystal structure of a larger fragment (TMEGF456) bound to thrombin both show that Met 388 is packed into the fifth domain. Using multidimensional NMR, we have solved the structure of TMEGF45 in which Met 388 is oxidized (TMEGF45ox) and the structure of TMEGF45 in which Met 388 is mutated to Leu (TMEGF45ML). Comparison of the structures shows that the fifth domain has a somewhat different structure depending on the residue at position 388, and several of the thrombin-binding residues are packed into the fifth domain in the oxidized protein while they are exposed and free to interact with thrombin in the native structure and the Met-Leu mutant. This observation is consistent with kinetic measurements showing that the K(m) for TMEGF45ox binding to thrombin is 3.3-fold higher than for the native protein. Most importantly, the connection between the two domains, as indicated by interdomain NOEs, appears to be essential for activity. In the TMEGF45ox structure which has a reduced k(cat) for protein C activation by the thrombin-TMEGF45ox complex, interaction between the two domains is lost. Conversely, a tighter connection is observed between the two domains in TMEGF45ML, which has a higher k(cat) for protein C activation by the thrombin-TMEGF45ML complex.