NADPH oxidases in Eukaryotes: red algae provide new hints!

Proton channels in algae: reasons to be excited

A fundamental requirement of all eukaryotes is the ability to translocate protons across membranes. This is critical in bioenergetics, for compartmentalized metabolism, and to regulate intracellular pH (pH(i)) within a range that is compatible with cellular metabolism. Plants, animals, and algae utilize specialized transport machinery for membrane energization and pH homeostasis that reflects the prevailing ionic conditions in which they evolved. The recent characterization of H(+)-permeable channels in marine and freshwater algae has led to the discovery of novel functions for these transport proteins in both cellular pH homeostasis and sensory biology. Here we review the potential implications for understanding the origins and evolution of membrane excitability and the phytoplankton-based marine ecosystem responses to ocean acidification.

Chlorophyll a and NADPH fluorescence lifetimes in the microalgae Haematococcus pluvialis (Chlorophyceae) under normal and astaxanthin-accumulating conditions

In vivo fluorescence lifetimes of chlorophyll-a (chl-a) and nicotinamide adenine dinucleotide phosphate (NADPH) were obtained from the green microalgae Haematococcus pluvialis under normal and nutrient-stressed conditions (green stage and red stage, respectively), using two-photon excitation provided by a laser generating pulses in the femtosecond range, and a Leica microscope setup. Analysis of the fluorescence lifetime decay curve revealed two separate lifetime components in all our measurements. A short-lifetime component for chl-a of ~250 ps was completely dominant, contributing more than 90% of overall intensity in both green-stage and red-stage cells. Green-stage cells inhibited by 3-(3,4-dichlorophenyl)-1,1-dimethyl-urea (DCMU) displayed a significant chl-a lifetime increase for the short component. However, this was not the case for red-stage cells, in which DCMU inhibition did not significantly affect the lifetime. For green-stage cells, we found a short NADPH (free) lifetime component at ~150 ps to be completely dominating, but for red-stage cells, a longer component (protein bound) at ~3 ns contributed as much as 35% of the total intensity. We hypothesize that the long lifetime component of NADPH is connected to photoprotection in the cells and coupled to production of astaxanthin. DCMU does not seem to affect the fluorescence lifetimes of NADPH.

Nox enzymes from fungus to fly to fish and what they tell us about Nox function in mammals

The production of reactive oxygen species (ROS) in a highly regulated fashion is a hallmark of members of the NADPH oxidase (Nox) family of enzymes. Nox enzymes are present in most eukaryotic groups such as the amebozoid, fungi, algae and plants, and animals, in which they are involved in seemingly diverse biological processes. However, a comprehensive survey of Nox functions throughout biology reveals common functional themes. Noxes are often activated in response to stressful conditions such as nutrient starvation, physical damage, or pathogen attack. Although the end result varies depending on the organism and tissue, Nox-produced ROS mediate the response to the adverse stimuli, such as innate immunity responses in plants and animals or cell differentiation in Dictyostelium, fungi, and plants. These responses involve ROS-mediated signaling mechanisms occurring at intracellular or cell-to-cell levels and sometimes involve cell wall or extracellular matrix cross-linking. Indeed, Noxes are involved in local and systemic signaling from plants to fish and in cross-linking of the plant hair-cell wall, synthesis of the nematode cuticle, and formation of the sea urchin fertilization envelope. The extensive use of Nox enzymes in biology to regulate cell-to-cell signaling and morphogenesis suggests that additional functions in mammalian signaling and development remain to be discovered.

Ras and Nox: Linked signaling networks?

Both Ras and Nox represent ancient gene families which control a broad range of cellular responses. Both families mediate signals governing motility, differentiation, and proliferation, and both inhabit overlapping subcellular microdomains. Yet little is known of the precise functional relationship between these two ubiquitous families. In this review, we examine the interface where these two large fields meet.

Free Fatty Acids and Methyl Jasmonate Trigger Defense Reactions in Laminaria digitata

Arachidonic acid, linolenic acid and methyl jasmonate (MeJA) were found to be strong triggers of an oxidative burst in the kelp Laminaria digitata. These findings constitute the first report of an oxidative burst in an algal system induced by free fatty acids. The source of reactive oxygen species can be at least partially inhibited by diphenylene iodonium (DPI). Treatment with arachidonic acid increases the levels of a number of free fatty acids [including myristic (C14:0), linoleic (C18:2), linolenic (C18:3) and eicosapentaeneoic (C20:5) acids] and hydroxylated derivatives [such as 15-hydroxyeicosatetraenoic acid (15-HETE), 13-hydroxyoctadecatrienoic acid (13-HOTE) and 15-hydroxyeicosapentaenoic acid (15-HEPE)]. Similar to a previous report of the function of an alginate oligosaccharide-triggered oxidative burst in the establishment of resistance in L. digitata against infection by its brown algal endophyte Laminariocolax tomentosoides, C20:4- and MeJA-induced oxidative bursts seem to be involved in establishing the same protection in L. digitata. Altogether, this study supports the notion that lipid oxidation signaling plays a key role in defense induction in marine brown algae.

Update of the Diatom EST Database: a new tool for digital transcriptomics

The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130 000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77 000 Thalassiosira pseudonana ESTs from seven libraries, derived from cells grown in different nutrient and stress regimes. The updated relational database incorporates results from statistical analyses such as log-likelihood ratios and hierarchical clustering, which help to identify differentially expressed genes under different conditions, and allow similarities in gene expression in different libraries to be investigated in a functional context. The database also incorporates links to the recently sequenced genomes of P. tricornutum and T. pseudonana, enabling an easy cross-talk between the expression pattern of diatom orthologs and the genome browsers. These improvements will facilitate exploration of diatom responses to conditions of ecological relevance and will aid gene function identification of diatom-specific genes and in silico gene prediction in this largely unexplored class of eukaryotes. The updated Diatom EST Database is available at http://www.biologie.ens.fr/diatomics/EST3.

NADPH oxidases NOX-1 and NOX-2 require the regulatory subunit NOR-1 to control cell differentiation and growth in Neurospora crassa

We have proposed that reactive oxygen species (ROS) play essential roles in cell differentiation. Enzymes belonging to the NADPH oxidase (NOX) family produce superoxide in a regulated manner. We have identified three distinct NOX subfamilies in the fungal kingdom and have shown that NoxA is required for sexual cell differentiation in Aspergillus nidulans. Here we show that Neurospora crassa NOX-1 elimination results in complete female sterility, decreased asexual development, and reduction of hyphal growth. The lack of NOX-2 did not affect any of these processes but led instead to the production of sexual spores that failed to germinate, even in the presence of exogenous oxidants. The elimination of NOR-1, an ortholog of the mammalian Nox2 regulatory subunit gp67(phox), also caused female sterility, the production of unviable sexual spores, and a decrease in asexual development and hyphal growth. These results indicate that NOR-1 is required for NOX-1 and NOX-2 functions at different developmental stages and establish a link between NOX-generated ROS and the regulation of growth. Indeed, NOX-1 was required for the increased asexual sporulation previously observed in mutants without catalase CAT-3. We also analyzed the function of the penta-EF calcium-binding domain protein PEF-1 in N. crassa. Deletion of pef-1 resulted in increased conidiation but, in contrast to what occurs in Dictyostelium discoideum, the mutation of this peflin did not suppress the phenotypes caused by the lack of NOX-1. Our results support the role of ROS as critical cell differentiation signals and highlight a novel role for ROS in regulation of fungal growth.

NADPH oxidases are involved in differentiation and pathogenicity in Botrytis cinerea

Nicotinamide adenine dinucleotide (NADPH) oxidases have been shown to be involved in various differentiation processes in fungi. We investigated the role of two NADPH oxidases in the necrotrophic phytopathogenic fungus, Botrytis cinerea. The genes bcnoxA and bcnoxB were cloned and characterized; their deduced amino acid sequences show high homology to fungal NADPH oxidases. Analyses of single and double knock-out mutants of both NADPH oxidase genes showed that both bcnoxA and bcnoxB are involved in formation of sclerotia. Both genes have a great impact on pathogenicity: whereas bcnoxB mutants showed a retarded formation of primary lesions, probably due to an impaired formation of penetration structures, bcnoxA mutants were able to penetrate host tissue in the same way as the wild type but were much slower in colonizing the host tissue. Double mutants showed an additive effect: they were aberrant in penetration and colonization of plant tissue and, therefore, almost nonpathogenic. To study the structure of the fungal Nox complex in more detail, bcnoxR (encoding a homolog of the mammalian p67(phox), a regulatory subunit of the Nox complex) was functionally characterized. The phenotype of DeltabcnoxR mutants is identical to that of DeltabcnoxAB double mutants, providing evidence that BcnoxR is involved in activation of both Bcnox enzymes.

Structure, regulation and evolution of Nox-family NADPH oxidases that produce reactive oxygen species

NADPH oxidases of the Nox family exist in various supergroups of eukaryotes but not in prokaryotes, and play crucial roles in a variety of biological processes, such as host defense, signal transduction, and hormone synthesis. In conjunction with NADPH oxidation, Nox enzymes reduce molecular oxygen to superoxide as a primary product, and this is further converted to various reactive oxygen species. The electron-transferring system in Nox is composed of the C-terminal cytoplasmic region homologous to the prokaryotic (and organelle) enzyme ferredoxin reductase and the N-terminal six transmembrane segments containing two hemes, a structure similar to that of cytochrome b of the mitochondrial bc(1) complex. During the course of eukaryote evolution, Nox enzymes have developed regulatory mechanisms, depending on their functions, by inserting a regulatory domain (or motif) into their own sequences or by obtaining a tightly associated protein as a regulatory subunit. For example, one to four Ca(2+)-binding EF-hand motifs are present at the N-termini in several subfamilies, such as the respiratory burst oxidase homolog (Rboh) subfamily in land plants (the supergroup Plantae), the NoxC subfamily in social amoebae (the Amoebozoa), and the Nox5 and dual oxidase (Duox) subfamilies in animals (the Opisthokonta), whereas an SH3 domain is inserted into the ferredoxin-NADP(+) reductase region of two Nox enzymes in Naegleria gruberi, a unicellular organism that belongs to the supergroup Excavata. Members of the Nox1-4 subfamily in animals form a stable heterodimer with the membrane protein p22(phox), which functions as a docking site for the SH3 domain-containing regulatory proteins p47(phox), p67(phox), and p40(phox); the small GTPase Rac binds to p67(phox) (or its homologous protein), which serves as a switch for Nox activation. Similarly, Rac activates the fungal NoxA via binding to the p67(phox)-like protein Nox regulator (NoxR). In plants, on the other hand, this GTPase directly interacts with the N-terminus of Rboh, leading to superoxide production. Here I describe the regulation of Nox-family oxidases on the basis of three-dimensional structures and evolutionary conservation.

Pathogen-induced defense and innate immunity in macroalgae

Animals and vascular plants are known to defend themselves facultatively against pathogens, with innate receptors mediating their resistance. Macroalgal defense against microorganisms, in contrast, has until recently been regarded mainly as constitutive. Indeed, many macroalgae appear to be chemically defended at constantly high levels, and this is possibly one of the reasons why the first evidence of pathogen-aroused resistance in a macroalga was detected only a decade ago. Here, I summarize the results of studies that indicate the existence of pathogen-activated or pathogen-induced macroalgal defense. Most indications so far come from molecular investigations, which revealed major functional similarities among the defense systems of distant macroalgal clades and the innate immune systems of vascular plants and metazoans. Homologies exist in the primary and secondary defense-activating signals, as well as in the enzymes that are involved and the cellular responses that are activated. This strongly suggests that innate immunity also exists in relatively distinct macroalgal clades. However, a macroalgal receptor still needs to be isolated and characterized, and the molecular concept of macroalgal receptor-mediated immunity needs to be complemented with an ecological perspective on pathogen-induced defense, to develop a joint neuroecological perspective on seaweed-microbe interactions.

Molecular evolution of Phox-related regulatory subunits for NADPH oxidase enzymes

Background

The reactive oxygen-generating NADPH oxidases (Noxes) function in a variety of biological roles, and can be broadly classified into those that are regulated by subunit interactions and those that are regulated by calcium. The prototypical subunit-regulated Nox, Nox2, is the membrane-associated catalytic subunit of the phagocyte NADPH-oxidase. Nox2 forms a heterodimer with the integral membrane protein, p22phox, and this heterodimer binds to the regulatory subunits p47phox, p67phox, p40phox and the small GTPase Rac, triggering superoxide generation. Nox-organizer protein 1 (NOXO1) and Nox-activator 1 (NOXA1), respective homologs of p47phox and p67phox, together with p22phox and Rac, activate Nox1, a non-phagocytic homolog of Nox2. NOXO1 and p22phox also regulate Nox3, whereas Nox4 requires only p22phox. In this study, we have assembled and analyzed amino acid sequences of Nox regulatory subunit orthologs from vertebrates, a urochordate, an echinoderm, a mollusc, a cnidarian, a choanoflagellate, fungi and a slime mold amoeba to investigate the evolutionary history of these subunits.

Results

Ancestral p47phox, p67phox, and p22phox genes are broadly seen in the metazoa, except for the ecdysozoans. The choanoflagellate Monosiga brevicollis, the unicellular organism that is the closest relatives of multicellular animals, encodes early prototypes of p22phox, p47phox as well as the earliest known Nox2-like ancestor of the Nox1-3 subfamily. p67phox- and p47phox-like genes are seen in the sea urchin Strongylocentrotus purpuratus and the limpet Lottia gigantea that also possess Nox2-like co-orthologs of vertebrate Nox1-3. Duplication of primordial p47phox and p67phox genes occurred in vertebrates, with the duplicated branches evolving into NOXO1 and NOXA1. Analysis of characteristic domains of regulatory subunits suggests a novel view of the evolution of Nox: in fish, p40phox participated in regulating both Nox1 and Nox2, but after the appearance of mammals, Nox1 (but not Nox2) became independent of p40phox. In the fish Oryzias latipes, a NOXO1 ortholog retains an autoinhibitory region that is characteristic of mammalian p47phox, and this was subsequently lost from NOXO1 in later vertebrates. Detailed amino acid sequence comparisons identified both putative key residues conserved in characteristic domains and previously unidentified conserved regions. Also, candidate organizer/activator proteins in fungi and amoeba are identified and hypothetical activation models are suggested.

Conclusion

This is the first report to provide the comprehensive view of the molecular evolution of regulatory subunits for Nox enzymes. This approach provides clues for understanding the evolution of biochemical and physiological functions for regulatory-subunit-dependent Nox enzymes.

Molecular evolution of the reactive oxygen-generating NADPH oxidase (Nox/Duox) family of enzymes

Background

NADPH-oxidases (Nox) and the related Dual oxidases (Duox) play varied biological and pathological roles via regulated generation of reactive oxygen species (ROS). Members of the Nox/Duox family have been identified in a wide variety of organisms, including mammals, nematodes, fruit fly, green plants, fungi, and slime molds; however, little is known about the molecular evolutionary history of these enzymes.

Results

We assembled and analyzed the deduced amino acid sequences of 101 Nox/Duox orthologs from 25 species, including vertebrates, urochordates, echinoderms, insects, nematodes, fungi, slime mold amoeba, alga and plants. In contrast to ROS defense enzymes, such as superoxide dismutase and catalase that are present in prokaryotes, ROS-generating Nox/Duox orthologs only appeared later in evolution. Molecular taxonomy revealed seven distinct subfamilies of Noxes and Duoxes. The calcium-regulated orthologs representing 4 subfamilies diverged early and are the most widely distributed in biology. Subunit-regulated Noxes represent a second major subdivision, and appeared first in fungi and amoeba. Nox5 was lost in rodents, and Nox3, which functions in the inner ear in gravity perception, emerged the most recently, corresponding to full-time adaptation of vertebrates to land. The sea urchin Strongylocentrotus purpuratus possesses the earliest Nox2 co-ortholog of vertebrate Nox1, 2, and 3, while Nox4 first appeared somewhat later in urochordates. Comparison of evolutionary substitution rates demonstrates that Nox2, the regulatory subunits p47phox and p67phox, and Duox are more stringently conserved in vertebrates than other Noxes and Nox regulatory subunits. Amino acid sequence comparisons identified key catalytic or regulatory regions, as 68 residues were highly conserved among all Nox/Duox orthologs, and 14 of these were identical with those mutated in Nox2 in variants of X-linked chronic granulomatous disease. In addition to canonical motifs, the B-loop, TM6-FAD, VXGPFG-motif, and extreme C-terminal regions were identified as important for Nox activity, as verified by mutational analysis. The presence of these non-canonical, but highly conserved regions suggests that all Nox/Duox may possess a common biological function remained in a long history of Nox/Duox evolution.

Conclusion

This report provides the first comprehensive analysis of the evolution and conserved functions of Nox and Duox family members, including identification of conserved amino acid residues. These results provide a guide for future structure-function studies and for understanding the evolution of biological functions of these enzymes.

Evidence for oxylipin synthesis and induction of a new polyunsaturated fatty acid hydroxylase activity in Chondrus crispus in response to methyljasmonate

Signaling cascades involving oxygenated derivatives (oxylipins) of polyunsaturated fatty acids (PUFAs) are known to operate in response to external stimuli. The marine red alga Chondrus crispus uses both oxygenated derivatives of C18 (octadecanoids) and C20 (eicosanoids) PUFAs as developmental or defense hormones. The present study demonstrates that methyljasmonate (MeJA) triggers a cascade of oxidation of PUFAs leading to the synthesis of prostaglandins and other oxygenated fatty acids. As a result of a lipoxygenase-like activation, MeJA induces a concomitant accumulation of 13-hydroxy-9Z,11E-octadecadienoic acid (13-HODE) and 13-oxo-9Z,11E-octadecadienoic acid (13-oxo-ODE) in a dose-dependent manner in C. crispus. Furthermore, MeJA increases the level of mRNA encoding a gluthatione S-transferase and induces the activity of a new enzyme catalyzing the regio- and stereoselective bisallylic hydroxylation of polyunsaturated fatty acids from C(18) to C(22). The enzyme selectively oxidized the omega minus 7 carbon position (omega-7) and generated the stereoselective (R)-hydroxylated metabolites with a large enantiomeric excess. The enzyme specificity for the fatty acid recognition was not dependent of the position of double bonds but at least requires a methylene interrupted double bond 1,4-pentadiene motif involving the omega-7 carbon.

Response of the transcriptome of the intertidal red seaweed Chondrus crispus to controlled and natural stresses

Intertidal seaweeds inhabit an inherently stressful environment with rapidly changing physical conditions with the turning tides. Many macroalgae are therefore very resistant to abiotic stress; however, the bases for this tolerance and the relative importance of different stressors are largely unknown. Here, the effects of stress on the transcriptome of the red seaweed Chondrus crispus were investigated using cDNA microarrays. The responses were studied after exposure to high light, high temperature, and hypo- and hyperosmotic conditions in the laboratory and compared with gene expression in nature at different stress loads: at high and low tide at solar noon, and during a cloudy and a sunny day, respectively. The study identifies key stress genes and marker genes for specific stressors. The data also provide an insight into the physiological effects of stress; for example, high light stress and high natural stress caused an increase in antioxidative proteins, suggesting an increased oxidative stress. Clustering analysis suggested that osmotic stress modulated the gene expression in nature under high-stress conditions and was thus the most significant natural stressor. The potential cross-talk between stress reactions and methyl jasmonate-induced responses was also investigated and is tentatively suggested to be mediated by reactive oxygen species.

Expression profiling of Chondrus crispus (Rhodophyta) after exposure to methyl jasmonate

Methyl jasmonate (MeJA) is a plant hormone important for the mediation of signals for developmental processes and defence reactions in higher plants. The effects of MeJA and the signalling pathways on other photosynthetic organism groups are largely unknown, even though MeJA may have very important roles. Therefore the effects of MeJA in a red alga were studied. A medium-scale expression profiling approach to identify genes regulated by MeJA in the red seaweed Chondrus crispus is described here. The expression profiles were studied 0, 2, 4, 6, 12, and 24 h after the addition of MeJA to the seawater surrounding the algae. The changes in the transcriptome were monitored using cDNA microarrays with 1920 different cDNA representing 1295 unique genes. The responses of selected genes were verified with real-time PCR and the correlation between the two methods was generally satisfying. The study showed that 6% of genes studied showed a response to the addition of MeJA and the most dynamic response was seen after 6 h. Genes that showed up-regulation included several glutathione S-transferases, heat shock protein 20, a xenobiotic reductase, and phycocyanin lyase. Down-regulated transcripts included glucose kinase, phosphoglucose isomerase, and a ribosomal protein. A comparison between different functional groups showed an up-regulation of stress-related genes and a down-regulation of genes involved in energy conversion and general metabolism. It is concluded that MeJA, or a related compound, has a physiological role as a stress hormone in red algae. This study represents to our knowledge the first analysis of gene expression using cDNA microarrays in a red macroalga.