Something old, something new, something borrowed; how the thermoacidophilic archaeon Sulfolobus solfataricus responds to oxidative stress

Ion accumulation in a protein nanocage: finding noisy temporal sequences using a genetic algorithm

Many pathogenic bacteria are able to survive attack by the host's immune system because of antioxidant systems that mitigate the effects of reactive oxygen species. Dps is a hollow 12-subunit protein nanocage that prevents oxidative damage by oxidizing and sequestering intracellular Fe(2+); the resulting Fe(3+) forms an iron oxyhydroxide nanoparticle in the cage interior. Charged sites on the protein nanocage create an electrostatic gradient that guides ions through well-defined pores that connect the cage interior with the surrounding solution and toward nucleation sites on the cage interior. In this study, we use all-atom molecular dynamics to simulate the motion of simple cations into the dodecameric cage formed by the Dps protein from Listeria monocytogenes. Ion trajectories are analyzed by using a novel, to our knowledge, genetic algorithm to determine the temporal sequence of ion-protein interactions. Ions enter Dps through well-defined pores at the ferritinlike C(3) axes, with negatively-charged residues on the outside of the cage forming a fairly well-defined entrance pathway. This method of trajectory analysis may be broadly applicable in situations where the spatial localization of ions or other small molecules is electrostatically driven by a biomolecule.

Multiple catalytically active thioredoxin folds: a winning strategy for many functions

The Thioredoxin (Trx) fold is a versatile protein scaffold consisting of a four-stranded β-sheet surrounded by three α-helices. Various insertions are possible on this structural theme originating different proteins, which show a variety of functions and specificities. During evolution, the assembly of different Trx fold domains has been used many times to build new multi-domain proteins able to perform a large number of catalytic functions. To clarify the interaction mode of the different Trx domains within a multi-domain structure and how their combination can affect catalytic performances, in this review, we report on a structural and functional analysis of the most representative proteins containing more than one catalytically active Trx domain: the eukaryotic protein disulfide isomerases (PDIs), the thermophilic protein disulfide oxidoreductases (PDOs) and the hybrid peroxiredoxins (Prxs).

Iron-sulfur world in aerobic and hyperthermoacidophilic archaea Sulfolobus

The general importance of the Fe-S cluster prosthetic groups in biology is primarily attributable to specific features of iron and sulfur chemistry, and the assembly and interplay of the Fe-S cluster core with the surrounding protein is the key to in-depth understanding of the underlying mechanisms. In the aerobic and thermoacidophilic archaea, zinc-containing ferredoxin is abundant in the cytoplasm, functioning as a key electron carrier, and many Fe-S enzymes are produced to participate in the central metabolic and energetic pathways. De novo formation of intracellular Fe-S clusters does not occur spontaneously but most likely requires the operation of a SufBCD complex of the SUF machinery, which is the only Fe-S cluster biosynthesis system conserved in these archaea. In this paper, a brief introduction to the buildup and maintenance of the intracellular Fe-S world in aerobic and hyperthermoacidophilic crenarchaeotes, mainly Sulfolobus, is given in the biochemical, genetic, and evolutionary context.

Peroxiredoxin: a central player in immune modulation

Peroxiredoxins (Prx) are a family of anti-oxidants that protect cells from metabolically produced reactive oxygen species (ROS). The presence of these enzymes in the secretomes of many parasitic helminths suggests they provide protection against ROS released by host immune effector cells. However, we recently reported that helminth-secreted Prx also contribute to the development of Th2-responses via a mechanism involving the induction of alternatively activated macrophages. In this review, we discuss the role helminth Prx may play in modulating the immune responses of their hosts.

Life in blue: copper resistance mechanisms of bacteria and archaea used in industrial biomining of minerals

Industrial biomining processes to extract copper, gold and other metals involve the use of extremophiles such as the acidophilic Acidithiobacillus ferrooxidans (Bacteria), and the thermoacidophilic Sulfolobus metallicus (Archaea). Together with other extremophiles these microorganisms subsist in habitats where they are exposed to copper concentrations higher than 100mM. Herein we review the current knowledge on the Cu-resistance mechanisms found in these microorganisms. Recent information suggests that biomining extremophiles respond to extremely high Cu concentrations by using simultaneously all or most of the following key elements: 1) a wide repertoire of Cu-resistance determinants; 2) duplication of some of these Cu-resistance determinants; 3) existence of novel Cu chaperones; 4) a polyP-based Cu-resistance system, and 5) an oxidative stress defense system. Further insight of the biomining community members and their individual response to copper is highly relevant, since this could provide key information to the mining industry. In turn, this information could be used to select the more fit members of the bioleaching community to attain more efficient industrial biomining processes.

Histidine is a source of the antioxidant, alpha-ketoglutarate, in Pseudomonas fluorescens challenged by oxidative stress

The role of alpha-ketoglutarate (KG) in the detoxification of reactive oxygen species (ROS) has only recently begun to be appreciated. This ketoacid neutralizes ROS in an NADPH-independent manner with the concomitant formation of succinate and CO(2). To further probe this intriguing attribute of KG in living systems, we have evaluated the significance of histidine metabolism in the model organism, Pseudomonas fluorescens, challenged by hydrogen peroxide (H(2)O(2)). Here, we show that this amino acid does contribute to KG homeostasis and appears to be earmarked for the production of KG during oxidative stress. Both the NAD- and the NADP-dependent glutamate dehydrogenases were upregulated in the stressed cells despite the sharp decline in the activities of numerous enzymes mediating the tricarboxylic acid cycle and oxidative phosphorylation. Enzymes such as isocitrate dehydrogenase-NAD dependent, succinate dehydrogenase, alpha-ketoglutarate dehydrogenase, Complex I, and Complex IV were severely affected in the P. fluorescens grown in the presence of H(2)O(2). Studies with fluorocitrate, a potent inhibitor of citrate metabolism, clearly revealed that histidine was preferentially utilized in the production of KG in the H(2)O(2)-challenged cells. Regulation experiments also helped confirm that the metabolic reprogramming, resulting in the enhanced production of KG was induced by H(2)O(2) stress. These data further establish the pivotal role that KG plays in antioxidative defense.

Selective depletion of Sulfolobus solfataricus transcription factor E under heat shock conditions

Archaeal transcriptional machinery is similar to that of eukaryotes. We studied the fates of various components of the Sulfolobus solfataricus transcriptional apparatus under different stresses and found that in cells incubated at 90 degrees C for 1 h, transcription factor E (TFE) is selectively depleted, but its mRNA levels are increased. We discuss the implications of these findings.

Inducible and constitutive promoters for genetic systems in Sulfolobus acidocaldarius

Central to genetic work in any organism are the availability of a range of inducible and constitutive promoters. In this work we studied several promoters for use in the hyperthermophilic archaeon Sulfolobus acidocaldarius. The promoters were tested with the aid of an E. coli-Sulfolobus shuttle vector in reporter gene experiments. As the most suitable inducible promoter a maltose inducible promoter was identified. It comprises 266 bp of the sequence upstream of the gene coding for the maltose/maltotriose binding protein (mbp, Saci_1165). Induction is feasible with either maltose or dextrin at concentrations of 0.2-0.4%. The highest increase in expression (up to 17-fold) was observed in late exponential and stationary phase around 30-50 h after addition of dextrin. Whereas in the presence of glucose and xylose higher basal activity and reduced inducibility with maltose is observed, sucrose can be used in the growth medium additionally without affecting the basal activity or the inducibility. The minimal promoter region necessary could be narrowed down to 169 bp of the upstream sequence. The ABCE1 protein from S. solfataricus was successfully expressed under control of the inducible promoter with the shuttle vector pC and purified from the S. acidocaldarius culture with a yield of about 1 mg L(-1) culture. In addition we also determined the promoter strength of several constitutive promoters.