The first structure of a cold-adapted superoxide dismutase (SOD): biochemical and structural characterization of iron SOD from Aliivibrio salmonicida

Distinct gut microbial communities and functional predictions in divergent ophiuroid species: host differentiation, ecological niches, and adaptation to cold-water habitats

IMPORTANCE

Gastrointestinal microorganisms are critical to the survival and adaptation of hosts, and there are few studies on the differences and functions of gastrointestinal microbes in widely distributed species. This study investigated the gut microbes of two ophiuroid species (Ophiura sarsii and its subspecies O. sarsii vadicola) in cold-water habitats of the Northern Pacific Ocean. The results showed that a combination of host and environmental factors shapes the intestinal microbiota of ophiuroids. There was a high similarity in microbial communities between the two groups living in different regions, which may be related to their similar ecological niches. These microorganisms played a vital role in the ecological success of ophiuroids as the foundation for their adaptation to cold-water environments. This study revealed the complex relationship between hosts and their gut microbes, providing insights into the role they play in the adaptation and survival of marine species.

Advances in cold-adapted enzymes derived from microorganisms

Cold-adapted enzymes, produced in cold-adapted organisms, are a class of enzyme with catalytic activity at low temperatures, high temperature sensitivity, and the ability to adapt to cold stimulation. These enzymes are largely derived from animals, plants, and microorganisms in polar areas, mountains, and the deep sea. With the rapid development of modern biotechnology, cold-adapted enzymes have been implemented in human and other animal food production, the protection and restoration of environments, and fundamental biological research, among other areas. Cold-adapted enzymes derived from microorganisms have attracted much attention because of their short production cycles, high yield, and simple separation and purification, compared with cold-adapted enzymes derived from plants and animals. In this review we discuss various types of cold-adapted enzyme from cold-adapted microorganisms, along with associated applications, catalytic mechanisms, and molecular modification methods, to establish foundation for the theoretical research and application of cold-adapted enzymes.

Tolerance of Pseudomonas strain to the 2,4-D herbicide through a peroxidase system

Herbicides are widely used in agricultural practices for preventing the proliferation of weeds. Upon reaching soil and water, herbicides can harm nontarget organisms, such as bacteria, which need an efficient defense mechanism to tolerate stress induced by herbicides. 2,4-Dichlorophenoxyacetic acid (2,4-D) is a herbicide that exerts increased oxidative stress among bacterial communities. Bacterial isolates were obtained from the biofilm of tanks containing washing water from the packaging of different pesticides, including 2,4-D. The Pseudomonas sp. CMA-7.3 was selected because of its tolerance against 2,4-D toxicity, among several sensitive isolates from the biofilm collection. This study aimed to evaluate the antioxidative response system of the selected strain to 2,4-D. It was analyzed the activity of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), and guaiacol peroxidase GPX enzymes, that are poorly known in the literature for bacterial systems. The Pseudomonas sp. CMA-7.3 presented an efficient response system in balancing the production of hydrogen peroxide, even at 25x the dose of 2,4-D used in agriculture. The antioxidative system was composed of Fe–SOD enzymes, less common than Mn–SOD in bacteria, and through the activities of KatA and KatB isoforms, working together with APX and GPX, having their activities coordinated possibly by quorum sensing molecules. The peroxide control is poorly documented for bacteria, and this work is unprecedented for Pseudomonas and 2,4-D. Not all bacteria harbor efficient response system to herbicides, therefore they could affect the diversity and functionality of microbiome in contaminated soils, thereby impacting agricultural production, environment sustainability and human health.

Herbicides Tolerance in a Pseudomonas Strain Is Associated With Metabolic Plasticity of Antioxidative Enzymes Regardless of Selection

Agriculture uses many food production chains, and herbicides participate in this process by eliminating weeds through different biochemical strategies. However, herbicides can affect non-target organisms such as bacteria, which can suffer damage if there is no efficient control of reactive oxygen species. It is not clear, according to the literature, whether the efficiency of this control needs to be selected by the presence of xenobiotics. Thus, the Pseudomonas sp. CMA 6.9 strain, collected from biofilms in an herbicide packaging washing tank, was selected for its tolerance to pesticides and analyzed for activities of different antioxidative enzymes against the herbicides Boral^®, absent at the isolation site, and Heat^®, present at the site; both herbicides have the same mode of action, the inhibition of the enzyme protoporphyrinogen oxidase. The strain showed tolerance to both herbicides in doses up to 45 times than those applied in agriculture. The toxicity of these herbicides, which is greater for Boral^®, was assessed by means of oxidative stress indicators, growth kinetics, viability, and amounts of peroxide and malondialdehyde. However, the studied strain showed two characteristic antioxidant response systems for each herbicide: glutathione-s-transferase acting to control malondialdehyde in treatments with Boral^®; and catalase, ascorbate peroxidase, and guaiacol peroxidase in the control of peroxide induced by Heat^®. It is possible that this modulation of the activity of different enzymes independent of previous selection characterizes a system of metabolic plasticity that may be more general in the adaptation of microorganisms in soil and water environments subjected to chemical contaminants. This is relevant to the impact of pesticides on the diversity and abundance of microbial species as well as a promising line of metabolic studies in microbial consortia for use in bioremediation.

Regulation of Mitochondrial Dynamics in Parkinson's Disease-Is 2-Methoxyestradiol a Missing Piece?

Mitochondria, as "power house of the cell", are crucial players in cell pathophysiology. Beyond adenosine triphosphate (ATP) production, they take part in a generation of reactive oxygen species (ROS), regulation of cell signaling and cell death. Dysregulation of mitochondrial dynamics may lead to cancers and neurodegeneration; however, the fusion/fission cycle allows mitochondria to adapt to metabolic needs of the cell. There are multiple data suggesting that disturbed mitochondrial homeostasis can lead to Parkinson's disease (PD) development. 2-methoxyestradiol (2-ME), metabolite of 17β-estradiol (E2) and potential anticancer agent, was demonstrated to inhibit cell growth of hippocampal HT22 cells by means of nitric oxide synthase (NOS) production and oxidative stress at both pharmacologically and also physiologically relevant concentrations. Moreover, 2-ME was suggested to inhibit mitochondrial biogenesis and to be a dynamic regulator. This review is a comprehensive discussion, from both scientific and clinical point of view, about the influence of 2-ME on mitochondria and its plausible role as a modulator of neuron survival.

Crystal structure of an iron superoxide dismutase from the pathogenic amoeba Acanthamoeba castellanii

The iron superoxide dismutase found in the pathogenic amoeba Acanthamoeba castellanii (AcFeSOD) may play essential roles in the survival of the parasite, not only by protecting it from endogenous oxidative stress but also by detoxifying oxidative killing of the parasite by host immune effector cells. The AcFeSOD protein was expressed in a stable form using an Escherichia coli expression system and was crystallized by the microbatch and hanging-drop vapour-diffusion methods. The structure was determined to 2.33 Å resolution from a single AcFeSOD crystal. The crystal belonged to the hexagonal space group P61 and contained 12 molecules forming three tetramers in the asymmetric unit, with an iron ion bound in each molecule. Structural comparisons and sequence alignment of AcFeSOD with other FeSODs showed a well conserved overall fold and conserved active-site residues with subtle differences.

Antarctic marine ciliates under stress: superoxide dismutases from the psychrophilic Euplotes focardii are cold-active yet heat tolerant enzymes

Oxidative stress is a particularly severe threat to Antarctic marine polar organisms because they are exposed to high dissolved oxygen and to intense UV radiation. This paper reports the features of three superoxide dismutases from the Antarctic psychrophilic ciliate Euplotes focardii that faces two environmental challenges, oxidative stress and low temperature. Two out of these are Cu,Zn superoxide dismutases (named Ef-SOD1a and Ef-SOD1b) and one belongs to the Mn-containing group (Ef-SOD2). Ef-SOD1s and Ef-SOD2 differ in their evolutionary history, expression and overall structural features. Ef-SOD1 genes are expressed at different levels, with Ef-SOD1b mRNA 20-fold higher at the ciliate optimal temperature of growth (4 °C). All Ef-SOD enzymes are active at 4 °C, consistent with the definition of cold-adapted enzymes. At the same time, they display temperatures of melting in the range 50-70 °C and retain residual activity after incubation at 65-75 °C. Supported by data of molecular dynamics simulation, we conclude that the E. focardii SODs combine cold activity, local molecular flexibility and thermo tolerance.

Tolerance analysis of chloroplast OsCu/Zn-SOD overexpressing rice under NaCl and NaHCO3 stress

The 636-bp-long cDNA sequence of OsCu/Zn-SOD (AK059841) was cloned from Oryza sativa var. Longjing11 via reverse transcription polymerase chain reaction (RT-PCR). The encoded protein comprised of 211 amino acids is highly homologous to Cu/Zn-SOD proteins from tuscacera rice and millet. Quantitative RT-PCR revealed that in rice, the level of OsCu/Zn-SOD gene expression was lowest in roots and was highest in petals and during the S5 leaf stage. Moreover, the expression level of OsCu/Zn-SOD gene expression decreased during the L5 leaf stage to maturity. The level of OsCu/Zn-SOD gene expression, however, was increased under saline–sodic stress and NaHCO₃ stress. Germination tests under 125, 150, and 175 mM NaCl revealed that OsCu/Zn-SOD-overexpressing lines performed better than the non-transgenic (NT) Longjing11 lines in terms of germination rate and height. Subjecting seedlings to NaHCO₃ and water stress revealed that OsCu/Zn-SOD-overexpressing lines performed better than NT in terms of SOD activity, fresh weight, root length, and height. Under simulated NaHCO₃ stress, OsCu/Zn-SOD-overexpressing lines performed better than NT in terms of survival rate (25.19% > 6.67%) and yield traits (average grain weight 20.6 > 18.15 g). This study showed that OsCu/Zn-SOD gene overexpression increases the detoxification capacity of reactive oxygen species in O. sativa and reduces salt-induced oxidative damage. We also revealed the regulatory mechanism of OsCu/Zn-SOD enzyme in saline–sodic stress resistance in O. sativa. Moreover, we provided an experimental foundation for studying the mechanism of OsCu/Zn-SOD enzymes in the chloroplast.

Discovery, Molecular Mechanisms, and Industrial Applications of Cold-Active Enzymes

Cold-active enzymes constitute an attractive resource for biotechnological applications. Their high catalytic activity at temperatures below 25°C makes them excellent biocatalysts that eliminate the need of heating processes hampering the quality, sustainability, and cost-effectiveness of industrial production. Here we provide a review of the isolation and characterization of novel cold-active enzymes from microorganisms inhabiting different environments, including a revision of the latest techniques that have been used for accomplishing these paramount tasks. We address the progress made in the overexpression and purification of cold-adapted enzymes, the evolutionary and molecular basis of their high activity at low temperatures and the experimental and computational techniques used for their identification, along with protein engineering endeavors based on these observations to improve some of the properties of cold-adapted enzymes to better suit specific applications. We finally focus on examples of the evaluation of their potential use as biocatalysts under conditions that reproduce the challenges imposed by the use of solvents and additives in industrial processes and of the successful use of cold-adapted enzymes in biotechnological and industrial applications.

Structure analysis of a glycosides hydrolase family 42 cold-adapted β-galactosidase from Rahnella sp. R3

The β-galactosidase isolated from a psychrotrophic bacterium, Rahnella sp. R3 (R-β-Gal), exhibits high activity at low temperature and has potential in the dairy industry.

Biochemical characterization of psychrophilic Mn-superoxide dismutase from newly isolated Exiguobacterium sp. OS-77

Many types of superoxide dismutases have been purified and characterized from various bacteria, however, a psychrophilic Mn-superoxide dismutase (MnSOD) has not yet been reported. Here, we describe the purification and the biochemical characterization of the psychrophilic MnSOD from Exiguobacterium sp. strain OS-77 (EgMnSOD). According to 16S rRNA sequence analysis, a newly isolated bacterium strain OS-77 belongs to the genus Exiguobacterium. The optimum growth temperature of the strain OS-77 is 20 °C. The EgMnSOD is a homodimer of 23.5 kDa polypeptides determined by SDS-PAGE and gel filtration analysis. UV-Vis spectrum and ICP-MS analysis clearly indicated that the homogeneously purified enzyme contains only a Mn ion as a metal cofactor. The optimal reaction pH and temperature of the enzyme were pH 9.0 and 5 °C, respectively. Notably, the purified EgMnSOD was thermostable up to 45 °C and retained 50% activity after 21.2 min at 60 °C. The differential scanning calorimetry also indicated that the EgMnSOD is thermostable, exhibiting two protein denaturation peaks at 65 and 84 °C. The statistical analysis of amino acid sequence and composition of the EgMnSOD suggests that the enzyme retains psychrophilic characteristics.

Detection, distribution and characterization of novel superoxide dismutases from Yersinia enterocolitica Biovar 1A

BACKGROUND

Superoxide dismutases (SODs) cause dismutation of superoxide radicals to hydrogen peroxide and oxygen. Besides protecting the cells against oxidative damage by endogenously generated oxygen radicals, SODs play an important role in intraphagocytic survival of pathogenic bacteria. The complete genome sequences of Yersinia enterocolitica strains show presence of three different sod genes. However, not much is known about the types of SODs present in Y. enterocolitica, their characteristics and role in virulence and intraphagocytic survival of this organism.

METHODOLOGY/PRINCIPAL FINDINGS

This study reports detection and distribution of the three superoxide dismutase (sodA, sodB and sodC) genes in 59 strains of Y. enterocolitica and related species. The majority (94%) of the strains carried all three genes and constitutive expression of sodA and sodB was detected in 88% of the strains. Expression of sodC was not observed in any of the strains. The sodA, sodB and sodC genes of Y. enterocolitica were cloned in pET28a (+) vector. Recombinant SodA (82 kDa) and SodB (21 kDa) were expressed as homotetramer and monomer respectively, and showed activity over a broad range of pH (3.0-8.0) and temperature (4-70°C). SodA and SodB showed optimal activity at 4°C under acidic pH of 6.0 and 4.0 respectively. The secondary structures of recombinant SodA and SodB were studied using circular dichroism. Production of YeSodC was not observed even after cloning and expression in E. coli BL21(DE3) cells. A SodA(-) SodB(-) Escherichia coli strain which was unable to grow in medium supplemented with paraquat showed normal growth after complementation with Y. enterocolitica SodA or SodB.

CONCLUSIONS/SIGNIFICANCE

This is the first report on the distribution and characterization of superoxide dismutases from Y. enterocolitica. The low pH optima of both SodA and SodB encoded by Y. enterocolitica seem to implicate their role in acidic environments such as the intraphagocytic vesicles.

Psychrophily and catalysis

Polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. Indeed, low temperatures have a negative effect on ectothermic populations since they can affect their growth, reaction rates of biochemical reactions, membrane permeability, diffusion rates, action potentials, protein folding, nucleic acids dynamics and other temperature-dependent biochemical processes. Since the discovery that these ecosystems, contrary to what was initially expected, sustain a rather high density and broad diversity of living organisms, increasing efforts have been dedicated to the understanding of the molecular mechanisms involved in their successful adaptation to apparently unfavorable physical conditions. The first question that comes to mind is: How do these organisms compensate for the exponential decrease of reaction rate when temperature is lowered? As most of the chemical reactions that occur in living organisms are catalyzed by enzymes, the kinetic and thermodynamic properties of cold-adapted enzymes have been investigated. Presently, many crystallographic structures of these enzymes have been elucidated and allowed for a rather clear view of their adaptation to cold. They are characterized by a high specific activity at low and moderate temperatures and a rather low thermal stability, which induces a high flexibility that prevents the freezing effect of low temperatures on structure dynamics. These enzymes also display a low activation enthalpy that renders them less dependent on temperature fluctuations. This is accompanied by a larger negative value of the activation entropy, thus giving evidence of a more disordered ground state. Appropriate folding kinetics is apparently secured through a large expression of trigger factors and peptidyl–prolyl cis/trans-isomerases.

Psychrophilic enzymes: from folding to function and biotechnology

Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Several open questions in the field are also highlighted.

Function and biotechnology of extremophilic enzymes in low water activity

Enzymes from extremophilic microorganisms usually catalyze chemical reactions in non-standard conditions. Such conditions promote aggregation, precipitation, and denaturation, reducing the activity of most non-extremophilic enzymes, frequently due to the absence of sufficient hydration. Some extremophilic enzymes maintain a tight hydration shell and remain active in solution even when liquid water is limiting, e.g. in the presence of high ionic concentrations, or at cold temperature when water is close to the freezing point. Extremophilic enzymes are able to compete for hydration via alterations especially to their surface through greater surface charges and increased molecular motion. These properties have enabled some extremophilic enzymes to function in the presence of non-aqueous organic solvents, with potential for design of useful catalysts. In this review, we summarize the current state of knowledge of extremophilic enzymes functioning in high salinity and cold temperatures, focusing on their strategy for function at low water activity. We discuss how the understanding of extremophilic enzyme function is leading to the design of a new generation of enzyme catalysts and their applications to biotechnology.

Structure and flexibility in cold-adapted iron superoxide dismutases: the case of the enzyme isolated from Pseudoalteromonas haloplanktis

Superoxide dismutases (SODs) are metalloenzymes catalysing the dismutation of superoxide anion radicals into molecular oxygen and hydrogen peroxide. Here, we present the crystal structure of a cold-adapted Fe-SOD from the Antarctic eubacterium Pseudoalteromonas haloplanktis (PhSOD), and that of its complex with sodium azide. The structures were compared with those of the corresponding homologues having a high sequence identity with PhSOD, such as the mesophilic SOD from Escherichia coli (EcSOD) or Pseudomonas ovalis, and the psychrophilic SOD from Aliivibrio salmonicida (AsSOD). These enzymes shared a large structural similarity, such as a conserved tertiary structure and arrangement of the two monomers, an almost identical total number of inter- and intramolecular hydrogen bonds and salt bridges. However, the two cold-adapted SODs showed an increased flexibility of the active site residues with respect to their mesophilic homologues. Structural information was combined with a characterisation of the chemical and thermal stability performed by CD and fluorescence measurements. Despite of its psychrophilic origin, the denaturation temperature of PhSOD was comparable with that of the mesophilic EcSOD, whereas AsSOD showed a lower denaturation temperature. On the contrary, the values of the denaturant concentration at the transition midpoint were in line with the psychrophilic/mesophilic origin of the proteins. These data provide additional support to the hypothesis that cold-adapted enzymes achieve efficient catalysis at low temperature, by increasing the flexibility of their active site; moreover, our results underline how fine structural modifications can alter enzyme flexibility and/or stability without compromising the overall structure of typical rigid enzymes, such as SODs.

Extremophiles and their application to veterinary medicine

Extremophiles can be defined as organisms that can survive in extreme environments that cannot support mammalian life. They include microorganisms that can tolerate temperature extremes, extremes of pH, salinity, hydrostatic pressure and ionizing radiation, as well as low oxygen tension, desiccation and the presence of heavy metals. Psychrophilic organisms also include fish in polar waters and animals that withstand freezing. Rare examples of thermophilic pathogens exist, and the main category of extremophilic animal pathogens comprises psychrophilic and psychrotrophic microorganisms that cause fish diseases, e.g. Flavobacterium psychrophilum, Moritella viscosa, Aliivibrio wodanis and Aliivibrio salmonicida. The most widely known application of an extremophile product in veterinary medicine is DNA polymerase from thermophiles, which is a mainstay of PCR-based diagnostics for an extensive range of animal pathogens. DNA polymerases and other extremophile enzymes are also used in many molecular biology applications and animal genomics. Other extremophile products may find application in veterinary medicine in the future. These include enzymes in biosensors, compatible solutes in skin care products, drug excipients, treatments for respiratory disease, radioprotectants, peptide antibiotics, archaeal lipids for drug delivery and anti-cancer therapeutics.

Molecular adaptations to psychrophily: the impact of 'omic' technologies

The ability of cold-adapted microorganisms (generally referred to as psychrophiles) to survive is the result of molecular evolution and adaptations which, together, counteract the potentially deleterious effects of low kinetic energy environments and the freezing of water. These physiological adaptations are seen at many levels. Against a background of detailed comparative protein structural analyses, the recent surge of psychrophile proteome, genome, metagenome and transcriptome sequence data has triggered a series of sophisticated analyses of changes in global protein composition. These studies have revealed consistent and statistically robust changes in amino acid composition, interpreted as evolutionary mechanisms designed to destabilise protein structures, as well as identifying the presence of novel genes involved in cold adaptation.