Expression and regulation pattern of ferritin-like DpsA in the archaeon Halobacterium salinarum

Structure and mechanism of iron translocation by a Dps protein from Microbacterium arborescens

Dps (DNA protection during starvation) enzymes are a major class of dodecameric proteins that bacteria use to detoxify their cytosol through the uptake of reactive iron species. In the stationary growth phase of bacteria, Dps enzymes are primarily used to protect DNA by biocrystallization. To characterize the wild type Dps protein from Microbacterium arborescens that displays additional catalytic functions (amide hydrolysis and synthesis), we determined the crystal structure to a resolution of 2.05 Å at low iron content. The structure shows a single iron at the ferroxidase center coordinated by an oxo atom, one water molecule, and three ligating residues. An iron-enriched protein structure was obtained at 2 Å and shows the stepwise uptake of two hexahydrated iron atoms moving along channels at the 3-fold axis before a restriction site inside the channels requires removal of the hydration sphere. Supporting biochemical data provide insight into the regulation of this acylamino acid hydrolase. Moreover, the peroxidase activity of the protein was determined. The influence of iron and siderophores on the expression of acylamino acid hydrolase was monitored during several stages of cell growth. Altogether our data provide an interesting view of an unusual Dps-like enzyme evolutionarily located apart from the large Dps sequence clusters.

Coordination of frontline defense mechanisms under severe oxidative stress

Inference of an environmental and gene regulatory influence network (EGRIN_OS) by integrating transcriptional responses to H₂O₂ and paraquat (PQ) has revealed a multi-tiered oxidative stress (OS)-management program to transcriptionally coordinate three peroxidase/catalase enzymes, two superoxide dismutases, production of rhodopsins, carotenoids and gas vesicles, metal trafficking, and various other aspects of metabolism.

ChIP-chip, microarray, and survival assays have validated important architectural aspects of this network, identified novel defense mechanisms (including two evolutionarily distant peroxidase enxymes), and showed that general transcription factors of the transcription factor B family have an important function in coordinating the OS response (OSR) despite their inability to directly sense ROS.

A comparison of transcriptional responses to sub-lethal doses of H₂O₂ and PQ with predictions of these responses made by an EGRIN model generated earlier from responses to other environmental factors has confirmed that a significant fraction of the OSR is made up of a generalized component that is also observed in response to other stressors.

Analysis of active regulons within environment and gene regulatory influence network for OS (EGRIN_OS) across diverse environmental conditions has identified the specialized component of oxidative stress response (OSR) that is triggered by sub-lethal OS, but not by other stressors, including sub-inhibitory levels of redox-active metals, extreme changes in oxygen tension, and a sub-lethal dose of γ rays.

Reactive oxygen species (ROS), such as hydrogen peroxide (H₂O₂), superoxide (O₂⁻), and hydroxyl (OH⁻) radicals, are normal by-products of aerobic metabolism. Evolutionarily conserved mechanisms including detoxification enzymes (peroxidase/catalase and superoxide dismutase (SOD)) and free radical scavengers manage this endogenous production of ROS. OS is a condition reached when certain environmental stresses or genetic defects cause the production of ROS to exceed the management capacity. The damage to diverse cellular components including DNA, proteins, lipids, and carbohydrates resulting from OS (Imlay, 2003; Apel and Hirt, 2004; Perrone et al, 2008) is recognized as an important player in many diseases and in the aging process (Finkel, 2005).

We have applied a systems approach to characterize the OSR of an archaeal model organism, Halobacterium salinarum NRC-1. This haloarchaeon grows aerobically at 4.3 M salt concentration in which it routinely faces cycles of desiccation and rehydration, and increased ultraviolet radiation—both of which can increase the production of ROS (Farr and Kogoma, 1991; Oliver et al, 2001). We have reconstructed the physiological adjustments associated with management of excessive OS through the analysis of global transcriptional changes elicited by step exposure to growth sub-inhibitory and sub-lethal levels of H₂O₂ and PQ (a redox-cycling drug that produces O₂⁻; Hassan and Fridovich, 1979) as well as during subsequent recovery from these stresses. We have integrated all of these data into a unified model for OSR to discover conditional functional links between protective mechanisms and normal aspects of metabolism. Subsequent phenotypic analysis of gene deletion strains has verified the conditional detoxification functions of three putative peroxidase/catalase enzymes, two SODs, and the protective function of rhodopsins under increased levels of H₂O₂ and PQ. Similarly, we have also validated ROS scavenging by carotenoids and flotation by gas vesicles as secondary mechanisms that may minimize OS.

Given the ubiquitous nature of OS, it is not entirely surprising that most organisms have evolved similar multiple lines of defense—both passive and active. Although such mechanisms have been extensively characterized using other model organisms, our integrated systems approach has uncovered additional protective mechanisms in H. salinarum (e.g. two evolutionarily distant peroxidase/catalase enzymes) and revealed a structure and hierarchy to the OSR through conditional regulatory associations among various components of the response. We have validated some aspects of the architecture of the regulatory network for managing OS by confirming physical protein–DNA interactions of six transcription factors (TFs) with promoters of genes they were predicted to influence in EGRIN_OS. Furthermore, we have also shown the consequence of deleting two of these TFs on transcript levels of genes they control and survival rate under OS. It is notable that these TFs are not directly associated with sensing ROS, but, rather, they have a general function in coordinating the overall response. This insight would not have been possible without constructing EGRIN_OS through systems integration of diverse datasets.

Although it has been known that OS is a component of diverse environmental stress conditions, we quantitatively show for the first time that much of the transcriptional responses induced by the two treatments could indeed have been predicted using a model constructed from the analysis of transcriptional responses to changes in other environmental factors (UV and γ-radiation, light, oxygen, and six metals). However, using specific examples we also reveal the specific components of the OSR that are triggered only under severe OS. Notably, this model of OSR gives a unified perspective of the interconnections among all of these generalized and OS-specific regulatory mechanisms.

Complexity of cellular response to oxidative stress (OS) stems from its wide-ranging damage to nucleic acids, proteins, carbohydrates, and lipids. We have constructed a systems model of OS response (OSR) for Halobacterium salinarum NRC-1 in an attempt to understand the architecture of its regulatory network that coordinates this complex response. This has revealed a multi-tiered OS-management program to transcriptionally coordinate three peroxidase/catalase enzymes, two superoxide dismutases, production of rhodopsins, carotenoids and gas vesicles, metal trafficking, and various other aspects of metabolism. Through experimental validation of interactions within the OSR regulatory network, we show that despite their inability to directly sense reactive oxygen species, general transcription factors have an important function in coordinating this response. Remarkably, a significant fraction of this OSR was accurately recapitulated by a model that was earlier constructed from cellular responses to diverse environmental perturbations—this constitutes the general stress response component. Notwithstanding this observation, comparison of the two models has identified the coordination of frontline defense and repair systems by regulatory mechanisms that are triggered uniquely by severe OS and not by other environmental stressors, including sub-inhibitory levels of redox-active metals, extreme changes in oxygen tension, and a sub-lethal dose of γ rays.

Coordinating responses to iron and oxygen stress with DNA and mRNA promoters: The ferritin story

Combinations of DNA antioxidant response element and mRNA iron responsive element regulate ferritin expression in animals in response to oxidant and iron stress, or normal developmental signals. Ferritins are protein nanocages, found in animals, plants, bacteria, and archaea, that convert iron and oxygen to ferric oxy biominerals in the protein central cavity; the mineral traps potentially toxic reactants and concentrates iron for the future synthesis of other iron/heme proteins. Regulatory signals and the nanocage gene products are the same throughout biology, but the genetic mechanisms, DNA versus DNA + mRNA, vary. The number of genes, temporal regulation, tissue distribution in multi-cellular organisms, and gene product size (maxi-ferritins have 24 subunits and mini-ferritins, or Dps proteins, have 12 subunits and are restricted to bacteria and archaea) suggest an overwhelming diversity and variability. However, common themes of regulation and function are described which indicate not only that the three-dimensional protein structure and the functions of the ferritins are conserved, but also that broad features of genetic regulation are conserved relative to organismal and/or community needs. The analysis illustrates the centrality of the ferritins to life with iron and oxygen and models how Nature harnesses potentially dangerous chemistry for biology.

Proteomic analysis of acidic chaperones, and stress proteins in extreme halophile Halobacterium NRC-1: a comparative proteomic approach to study heat shock response

BACKGROUND

Halobacterium sp. NRC-1 is an extremely halophilic archaeon and has adapted to optimal growth under conditions of extremely high salinity. Its proteome is highly acidic with a median pI of 4.9, a unique characteristic which helps the organism to adapt high saline environment. In the natural growth environment, Halobacterium NRC-1 encounters a number of stressful conditions including high temperature and intense solar radiation, oxidative and cold stress. Heat shock proteins and chaperones play indispensable roles in an organism's survival under many stress conditions. The aim of this study was to develop an improved method of 2-D gel electrophoresis with enhanced resolution of the acidic proteome, and to identify proteins with diverse cellular functions using in-gel digestion and LC-MS/MS and MALDI-TOF approach.

RESULTS

A modified 2-D gel electrophoretic procedure, employing IPG strips in the range of pH 3-6, enabled improved separation of acidic proteins relative to previous techniques. Combining experimental data from 2-D gel electrophoresis with available genomic information, allowed the identification of at least 30 cellular proteins involved in many cellular functions: stress response and protein folding (CctB, PpiA, DpsA, and MsrA), DNA replication and repair (DNA polymerase A alpha subunit, Orc4/CDC6, and UvrC), transcriptional regulation (Trh5 and ElfA), translation (ribosomal proteins Rps27ae and Rphs6 of the 30 S ribosomal subunit; Rpl31eand Rpl18e of the 50 S ribosomal subunit), transport (YufN), chemotaxis (CheC2), and housekeeping (ThiC, ThiD, FumC, ImD2, GapB, TpiA, and PurE). In addition, four gene products with undetermined function were also identified: Vng1807H, Vng0683C, Vng1300H, and Vng6254. To study the heat shock response of Halobacterium NRC-1, growth conditions for heat shock were determined and the proteomic profiles under normal (42 degrees C), and heat shock (49 degrees C) conditions, were compared. Using a differential proteomic approach in combination with available genomic information, bioinformatic analysis revealed five putative heat shock proteins that were upregulated in cells subjected to heat stress at 49 degrees C, namely DnaJ, GrpE, sHsp-1, Hsp-5 and sHsp-2.

CONCLUSION

The modified 2-D gel electrophoresis markedly enhanced the resolution of the extremely acidic proteome of Halobacterium NRC-1. Constitutive expression of stress proteins and chaperones help the organism to adapt and survive under extreme salinity and other stress conditions. The upregulated expression pattern of putative chaperones DnaJ, GrpE, sHsp-1, Hsp-5 and sHsp-2 under elevated temperature clearly suggests that Halobacterium NRC-1 has a sophisticated defense mechanism to survive in extreme environments.