MBE Advance Access originally published online on January 10, 2008
Molecular Biology and Evolution 2008 25(3):507-516; doi:10.1093/molbev/msm276
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Research Articles |
Hydrogen Peroxide–Induced Gene Expression across Kingdoms: A Comparative Analysis
* Department of Plant Systems Biology, Flanders Institute for Biotechnology, Ghent, Belgium
Department of Molecular Genetics, Ghent University, Ghent, Belgium
E-mail: frank.vanbreusegem{at}psb.ugent.be.
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Abstract |
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Cells react to oxidative stress conditions by launching a defense response through the induction of nuclear gene expression. The advent of microarray technologies allowed monitoring of oxidative stress–dependent changes of transcript levels at a comprehensive and genome-wide scale, resulting in a series of inventories of differentially expressed genes in different organisms. We performed a meta-analysis on hydrogen peroxide (H2O2)–induced gene expression in the cyanobacterium Synechocystis PCC 6803, the yeast Saccharomyces cerevisiae and Schizosaccharomyces pombe, the land plant Arabidopsis thaliana, and the human HeLa cell line. The H2O2-induced gene expression in both yeast species was highly conserved and more similar to the A. thaliana response than that of the human cell line. Based on the expression characteristics of genuine antioxidant genes, we show that the antioxidant capacity of microorganisms and higher eukaryotes is differentially regulated. Four families of evolutionarily conserved eukaryotic proteins could be identified that were H2O2 responsive across kingdoms: DNAJ domain–containing heat shock proteins, small guanine triphosphate-binding proteins, Ca2+-dependent protein kinases, and ubiquitin-conjugating enzymes.
Key Words: oxidative stress • hydrogen peroxide • microarray • comparative transcriptomics • Synechocystis • yeast • Arabidopsis • H. sapiens
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Introduction |
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All aerobic organisms frequently experience endogenous and environmental conditions that provoke the accumulation of reactive oxygen species (ROS). Hydrogen peroxide (H2O2), superoxide (O2•–), and singlet oxygen are highly reactive molecules and, therefore, potentially harmful at higher concentrations. They can haphazardly assault proteins, lipids, DNA, and any other cellular component, thereby causing severe damage. Consequently, aerobic organisms have developed or adapted an efficient ROS scavenging machinery, involving enzymes such as superoxide dismutases (SODs) and catalases together with an extensive battery of nonenzymatic antioxidants (Halliwell 2006
).
Compared with other ROS, H2O2 is a relatively long-lived molecule (1 ms) that is able to diffuse across cell membranes (Bienert et al. 2006). This characteristic is compatible with its role as a signaling molecule during growth and development (Finkel and Holbrook 2000; Sauer et al. 2001; Neill et al. 2002; Van Breusegem and Dat 2006). The transduction of H2O2 signals into biologically relevant information is governed by sensors or receptors, mitogen-activated protein kinases, and transcription factors and has been suggested to be evolutionarily conserved (Toone and Jones 1998; Georgiou 2002; Liu et al. 2005). The best-known example is the apoptosis signal-regulating kinase 1/c-jun N-terminal kinase cascade that activates the AP-1 transcription factor through the oxidation of cysteine residues (Abate et al. 1990; Delauney et al. 2000; Shen and Liu 2006). In yeast, different H2O2 levels trigger independent signaling pathways (Vivancos et al. 2006). H2O2 signaling in plants is coordinated via a complex network that involves multiple protein kinases and transcription factors (Mittler et al. 2004; Miller and Mittler 2006; Kaminaka et al. 2006). The coordinated action of 2 redox-regulated transcription factors, TGACG motif-binding factor 1 and non-expressor of pathogenesis-related genes 1, is required for defense gene expression and systemic acquired disease resistance in Arabidopsis thaliana (Després et al. 2003; Mou et al. 2003).
Since recently, transcriptional changes can be monitored on a genome-wide scale by using different technologies, such as differential display, expressed sequence tag sequencing, serial analysis of gene expression, cDNA-amplified fragment length polymorphism, microarrays, and deep sequencing technologies (Lockhart and Winzeler 2000; Donson et al. 2002; Vandenabeele et al. 2003; Emrich et al. 2007). Such analysis has led to comprehensive inventories of genome-wide H2O2-related gene expression in bacteria (Escherichia coli and Bacillus subtilis), the cyanobacterium Synechocystis sp. strain PCC 6803, 2 yeast species (Saccharomyces cerevisiae and Schizosaccharomyces pombe), mouse (Mus musculus), fruit fly (Drosophila melanogaster), several human (Homo sapiens) cell lines, and 1 plant species (A. thaliana) (Gasch et al. 2000; Zheng et al. 2001; Chuang et al. 2002; Chen et al. 2003; Lee et al. 2003; Desaint et al. 2004; Girardot et al. 2004; Kobayashi et al. 2004; Li et al. 2004; Mostertz et al. 2004; Murray et al. 2004; Davletova et al. 2005; Kim et al. 2005; Vanderauwera et al. 2005). These gene expression studies clearly showed that increased cellular H2O2 levels have a considerable impact on the transcriptome of all species, by changing the expression of hundreds of genes. H2O2 not only affects genes involved in ROS detoxification but also drives the expression of genes involved in signal transduction, transcriptional regulation, and protein, carbohydrate or lipid metabolism, illustrating the complexity of the transcriptional response to H2O2.
We present a comparative transcriptome analysis that assesses, at a genome-wide scale, the similarity of the H2O2-dependent transcriptional response in evolutionarily distant species. Besides some species- or lineage-specific H2O2 responses, our analysis identified a confined set of similarly induced gene products in eukaryotes, with a strong conservation in yeast and Arabidopsis.
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Materials and Methods |
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Microarray and Protein Data Sets
Expression data of H2O2-induced genes were obtained from either Web sites or supplementary data of the corresponding articles: Synechocystis (Li et al. 2004
; available at http://jb.asm.org); the complete data set of S. cerevisiae and S. pombe from http://www-genome.stanford.edu/yeast_stress/data/rawdata/complete_dataset.txt and from ftp://ftp.sanger.ac.uk/pub/postgenomics/s_pombe/wtaverage.txt, respectively; the complete microarray data set of the human HeLa cell line from http://microarray-pubs.stanford.edu/human_stress/Home.shtml; and a completely processed data set of the microarray analysis in A. thaliana (Kim et al. 2005; http://www.blackwellpublishing.com/products/journals/suppmat/TPJ/TPJ2295/TPJ2295sm.htm). A 2-fold change cutoff was used to identify genes that were differentially expressed.
The protein data set consisted of sequences from 1 cyanobacterium (Synechocystis sp. strain PCC 6803), 2 yeasts (S. cerevisiae and S. pombe), 2 mammals (H. sapiens and M. musculus), and 2 plants (A. thaliana and rice [Oryza sativa]). Sequence information for all Synechocystis proteins was obtained from the National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov, release NC_0009111). Protein sequences from S. cerevisiae and S. pombe were retrieved from the Saccharomyces Genome Database (http://www.yeastgenome.org; release of August 2004) and Genome DataBase (http://www.genedb.org; release of November 2004), respectively. All protein sequences from H. sapiens (U25 NCBI 34 assembly) and M. musculus (U25 NCBI m33 assembly) were obtained from EnsEMBL (http://www.ensembl.org). Sequence information for Arabidopsis (release 5 January 2004; Wortman et al. 2003) and rice (release 2 April 2004; Yuan et al. 2003) was provided by The Institute for Genome Research. When multiple protein sequences were available for the same gene locus, the longest was retained.
Construction of Protein Families
Protein families were constructed by applying the Tribe-Markov clustering algorithm (Tribe-MCL) that uses graph-clustering methods and identifies clusters in a protein–protein similarity graph in a process that is sensitive to the density and the strength of the connections (Enright et al. 2002). A similarity matrix was generated from an all-against-all comparison using Blast (Altschul et al. 1997) with an E value threshold of 0.01. Clusters were formed with an inflation factor of 3.0. The original MCL algorithm was obtained from http://micans.org/mcl/, and more information concerning Tribe-MCl is also available at http://www.ebi.ac.uk/research/cgg/services/tribe/.
Significance Estimation Using Random Sampling
The significance of the number of stress-responsive gene families conserved between 2 species was estimated with random sampling. Briefly, for both species, the number of genes found in our analysis was randomly selected from all the genes present on the microarrays and the corresponding protein families were identified together with the number of conserved families. Based on 1,000 random sampling iterations, the significance of the observed overlap was estimated.
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Results and Discussion |
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TOPAbstractIntroductionMaterials and MethodsResults and DiscussionConclusionsAcknowledgementsReferences |
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Identification of Homologous Gene Products across Kingdoms
We compared H2O2-driven gene expression in evolutionarily distant species by performing a meta-analysis on publicly available microarray data sets from 5 completely sequenced and annotated species (Synechocystis PCC 6803, S. cerevisiae, S. pombe, H. sapiens, and A. thaliana). These 5 species were selected because the relevant microarray studies were available and, with the exception of the protista, they cross the different biological kingdoms, hence spanning a broad evolutionary distance (Margulis 1992
; Hedges and Kumar 2003).
A first necessary step was the identification of homologous gene products within the different organisms. Therefore, we clustered the protein sequences of the different species with Tribe-MCL. This algorithm allows a fast and accurate classification of large protein data sets into protein families and has multiple advantages over alternative protein clustering methods (Enright et al. 2002). Protein sequences of a second plant (O. sativa) and mammalian species (M. musculus) were included to improve the clustering outcome.
The clustering resulted in 16,207 protein families (containing more than 1 protein) encompassing 118,020 individual proteins in total. The different protein families were first evaluated according to size (protein number), species number, and species representation. Family size was opposite proportional to frequency of occurrence, with the majority (>95%) of all families smaller than 20 proteins (fig. 1A). Most protein families were restricted to 1 (3232; 20%) or 2 (9112; 56%) species, reflecting the large evolutionary distances between the species (fig. 1B). The species representation of all 16,207 protein families pointed to the existence of a limited set of highly conserved proteins (belonging to 244 protein families) that have a molecular function similar in Synechocystis and in eukaryotes, as well as to a substantial diversity among the different kingdoms (fig. 2). In addition, with this analysis, 1,244 conserved eukaryotic protein families were identified (fig. 2).
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Quality of the Tribe-MCL was further assessed by manual inspection of the phylogenetic profiles of several genuine antioxidant enzymes: SODs, catalases, and peroxiredoxins, all known to have an evolutionarily conserved function during ROS detoxification (Touati 1988
; Zámock
and Koller 1999; Rhee et al. 2005). As expected, protein sequences of SODs, catalases, and peroxiredoxins were contained within specific protein families (data not shown). Proteins with abundant domains, including protein kinase or DNA-binding domains were frequently found in larger, more divergent protein families containing more than 200 proteins (Riechmann et al. 2000; Wang et al. 2003). Because Tribe-MCL correctly grouped proteins with significant sequence similarity and almost identical functions, we concluded that the clustering in protein families was accurate and reliable for further analysis.
H2O2-Induced Gene Expression in Evolutionarily Distant Species
For prokaryotes, we selected a microarray experiment that followed the expression of 3,168 genes from Synechocystis sp. strain PCC 6803 after addition of 1.5 mM H2O2 to a cell culture (Li et al. 2004). In the yeast experiments, cDNA microarrays (containing ca. 5,200 and 6,000 S. pombe and S. cerevisiae genes, respectively) were used to monitor gene expression after addition of H2O2 (0.3–0.5 mM) to a cell culture (Gasch et al. 2000; Chen et al. 2003). To avoid an additional level of complexity related to tissue-specific responses in multicellular organisms, single-cell systems were also used to study H2O2-induced stress responses in animals and plants. For H. sapiens, we selected a microarray analysis of 25,802 genes in HeLa cells treated with different H2O2 concentrations (Murray et al. 2004). For the plant kingdom, we opted for an experiment in which microarrays (representing 25,636 genes) were used to monitor the transcriptional changes of 2-week-old, liquid-cultured A. thaliana seedlings that were treated with 5 mM H2O2 (Kim et al. 2005). More details on the selected microarray experiments can be found in table 1. Due to the heterogeneity of the experimental setups, we used relative expression data to identify differentially expressed genes. Figure 3 presents the kinetics of the transcription response, showing the number of genes with 2-, 3-, 4-, and more than 5-fold changes within these experiments. In all species, a significant up- and downregulation of transcript levels occurred, but we focused only on the inductive response because, in most cases, it starts earlier than the repressed response, enabling one to target upstream genes with minimal interference of secondary effects. Within the early time points, we selected those at which the strongest induction was observed: 30 min, 30 min, 1 h, 6 h, and 3 h for Synechocystis, S. cerevisiae, S. pombe, human HeLa cell lines, and A. thaliana, respectively. Genes with an H2O2-induced expression of at least 2-fold were retained for further analysis (161, 607, 578, 298, and 690 genes for Synechocystis, S. cerevisiae, S. pombe, human HeLa cell line, and A. thaliana, respectively).
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H2O2-Response Matrix as a Tool for Comparing Gene Expression
First, we identified H2O2-responsive protein families. Within a species, a protein family was considered to be responsive when at least 1 of its members was more than 2-fold upregulated. A H2O2-response matrix was obtained that indicated how many gene products within each family were responsive. The data can be queried on our Web site (http://bioinformatics.psb.ugent.be/supplementary_data/strob/h2o2/). The number of H2O2-responsive families varied for each species and was proportional to the total number of H2O2-responsive genes. In S. cerevisiae, S. pombe, and A. thaliana, approximately 400 families were responsive to H2O2, in contrast to only 101 and 168 families in Synechocystis and H. sapiens, respectively (table 1). We used the H2O2-response matrix to determine the evolutionary conservation of the H2O2 response in all species (fig. 4A). The H2O2 responsiveness of 87% of the 1,253 families was restricted to 1 species, indicating a strong species-specific response (fig. 4B). Table 2 presents the pairwise overlap of the H2O2 response between the different species. Not surprisingly, the overlap was the largest between S. cerevisiae and S. pombe with 107 common H2O2-responsive protein families (P value <0.001), revealing that the H2O2-induced transcriptional response is highly conserved between these 2 yeasts. Our data, together with the conserved core environmental stress responses of distant yeast species, indicate that stress responses in general are well conserved in yeast (Chen et al. 2003
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Four Protein Families within the Core Eukaryotic H2O2 Response
In addition to protein families that were H2O2 responsive in only 2 species, 31 protein families were responsive in at least 3 species (table 3). Remarkably, 23 families were responsive in A. thaliana, S. cerevisiae, and S. pombe, but only 6 families were responsive in H. sapiens and both yeasts (fig 4C and D). Although the low number of H2O2-responsive families in H. sapiens is partially responsible for this difference, the conservation between both yeasts and A. thaliana was significant (P value <0.05) and that with H. sapiens was not. These data demonstrate that the transcriptional response to increased H2O2 levels in yeast is more similar to that of plants than to that of animals.
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Three protein families (representing guanine triphosphate [GTP]-binding proteins, protein kinases, or ubiquitin [Ub]-conjugating enzymes) were induced in yeast, A. thaliana, and H. sapiens but had no homologs in the prokaryote Synechocystis, restricting this conservation to eukaryotes. One protein family, representing DNAJ heat shock proteins (HSPs), was induced by H2O2 in all kingdoms. Together, these 4 protein families were defined as the "core eukaryotic H2O2 response." In the remaining protein families, no conserved response was found within 1 of the above-mentioned species combinations.
It is known that HSPs, GTP-binding proteins, protein kinases, and Ub-conjugating enzymes function in evolutionarily conserved biological processes, such as heat shock response, cellular signaling, or protein metabolism. Therefore, they might also have an important and conserved role in responses to oxidative stimuli. This analysis suggests that this conserved functionality requires, at least to some extent, regulation at the transcriptional level.
Evolutionarily Conserved H2O2-Induced Heat Shock Response
The proteins with the best evolutionarily conserved response to H2O2 are DNAJ HSPs, which are molecular chaperones defined by the presence of the conserved J domain (table 3). They can stimulate the substrate-binding activity of 70-kDa HSPs, thereby modulating accurate protein folding and transport (Walsh et al. 2004). Other HSPs (HSP90 and HSP20) were also, albeit less conserved, induced by H2O2 (table 3). In addition, H2O2 induction of HSPs has been reported in other species, such as tomato, rice, and Drosophila (Courgeon et al. 1990; Banzet et al. 1998; Lee et al. 2000). The conserved need for HSPs during oxidative stress might be explained by the chaperone function that HSPs can exert on oxidatively damaged and partially denatured proteins (Jakob et al. 1999). Alternatively, heat shock factors can act as direct sensors of H2O2, thereby regulating the expression of defense genes and subsequent protection during oxidative stress (Ahn and Thiele 2003; Volkov et al. 2006; Miller and Mittler 2006). Because of their protective function, loss of HSPs leads to increased sensitivity, whereas constitutive expression of some HSPs (such as chloroplastic HSP21) enhances the tolerance toward heat and H2O2 stress (Härndahl et al. 1999; Jakob et al. 1999; Ahn and Thiele 2003; Neta-Sharir et al. 2005). Together, these observations suggest a significant overlap between the heat shock and oxidative stress response in all kingdoms.
Eukaryotic H2O2 Signaling Involves Induction of G Proteins and Ca2+-Dependent Protein Kinases
We observed a conserved H2O2 induction in S. pombe, S. cervisiae, A. thaliana, and H. sapiens for 1 family of small, ras-like GTP-binding proteins (G proteins) and 1 protein family containing calcium (Ca2+)-dependent protein kinases (table 3). Both ras-like G proteins and protein kinases have already been implicated in oxidative stress signaling in yeast, plants, and mammals, suggesting a conserved function for such proteins (Toone and Jones 1998; Finkel and Holbrook 2000; Essers et al. 2004; Rentel et al. 2004). Closer investigation of the G-protein family revealed that it represents Rab GTP–binding proteins, 1 of the 5 subfamilies of ras-like GTPases (Vernoud et al. 2003). Rab GTPases are mainly involved in cellular trafficking, but at least in plants, they might have evolved additional functions (Rutherford and Moore 2002). However, a role for Rab proteins during oxidative stress signaling has not been elucidated yet.
Environmental or cellular stimuli, including oxidative stress, can cause changes in Ca2+ patterns, which can be sensed by specific Ca2+-dependent protein kinases and decoded into downstream effects, such as altered protein phosphorylation and gene expression (Cheng et al. 2002). In animals, it is well known that H2O2 can activate Ca2+-dependent protein kinases to prevent oxidative stress–induced cell death (Franklin et al. 2006).
In addition to the importance of G proteins and Ca2+-dependent protein kinases in controlling the eukaryotic response to oxidative stress, our data suggest the involvement of transcriptional regulation of these genes by H2O2, which might be essential for signal amplification and cross talk during oxidative stress. This hypothesis would be in agreement with the general function of ras-like G proteins and protein kinases in multiple, interconnected signaling cascades that control various biological processes (Matozaki et al. 2000).
Conserved H2O2-Induced Ubiquitination Response in Eukaryotes
Ub-conjugating enzymes act within proteasome-dependent proteolysis where they transfer Ub molecules, either directly or via an Ub ligase, to a substrate protein, a process known as ubiquitination (Pickart 2001). Transcripts of Ub-conjugating enzymes were induced by H2O2 in all 4 eukaryotes (table 3). A robust ubiquitination response and a transient increase in activity of the Ub-dependent pathway have been demonstrated to occur in lens cells exposed to oxidative stress, resulting in enhanced recovery after oxidative stress (Shang et al. 1997). This protection is probably a result of the targeted removal of oxidized or damaged proteins by Ub-conjugating enzymes or the Ub-dependent proteolytic pathway in general (Shang and Taylor 1995). The importance of the Ub-dependent pathway during oxidative stress is further highlighted by the requirement of a functional polyubiquitin gene to withstand toxic H2O2 levels in yeast (Cheng et al. 1994).
A Conserved Antioxidant Response in Unicellular Organisms
Besides 4 protein families with a conserved H2O2 induction in eukaryotes, we also observed a significant (P value <0.05) conservation within all the unicellular organisms, with 2 families showing a specific transcriptional induction in Synechocystis, S. cerevisiae, and S. pombe: short-chain dehydrogenases/reductases (SDR) and type I peroxiredoxins (table 3). Both SDR and peroxiredoxins are evolutionarily conserved proteins that are directly involved in the protection of cells against oxidative stress (Kallberg et al. 2002; Rhee et al. 2005). For example, constitutive expression of a SDR protein confers protection against oxidative stress-induced cell death via the detoxification of highly reactive xenobiotics (Botella et al. 2004). Peroxiredoxins are thioredoxin-dependent peroxidases that remove H2O2 and peroxinitrites (Rhee et al. 2005). The importance of peroxiredoxins as antioxidants is further illustrated by their capacity to prevent H2O2-induced apoptosis in human cells (Yuan et al. 2004).
In addition to SDR and type I peroxiredoxins, H2O2 induction of genuine antioxidant enzymes, such as catalases, SODs, glutathione peroxidases, ascorbate peroxidases, and type II peroxiredoxins, was also restricted to unicellular organisms (table 4). Catalases, copper/zinc (Cu/Zn) SODs, and glutathione peroxidases were induced in both yeast species but not in Synechocystis. Other antioxidant enzymes showed less conserved expression patterns in unicellular organisms. However, none of the antioxidant genes were induced by H2O2 in A. thaliana and H. sapiens. These data indicate that unicellular antioxidant systems are part of the oxidative stress-inducible adaptive responses, whereas higher eukaryotes carry a rather constitutive transcriptional antioxidant response during H2O2-induced oxidative stress (Storz and Imlay 1999). Although transcriptional control of antioxidant genes in specific (oxidative) stress situations cannot be excluded, antioxidant gene expression of animals and plants seems to be controlled at the posttranscriptional level. Manganese (Mn) SOD production in animal models, for example, is regulated via the binding of an unidentified MnSOD mRNA-binding molecule (Clerch 2000). In plants, posttranscriptional regulation of ascorbate peroxidase levels has been evidenced during programmed cell death and drought stress (Mittler and Zilinskas 1994; Mittler et al. 1998). Recently, a microRNA molecule (miR398) has been identified as a repressor of Cu/ZnSOD expression in A. thaliana and downregulation of miR398 is important for tolerance against oxidative stress (Sunkar et al. 2006). These data suggest that posttranscriptional control of antioxidant gene expression might be very important in mammals and plants.
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Conserved H2O2 Induction of Protein Families with Unknown Function
To investigate the H2O2 response of genes with unknown function, we manually analyzed our set of 162 different protein families that were responsive in at least 2 species for the overrepresentation of unknown, expressed, or hypothetical proteins. Because most unknown proteins are species-specific, only 18 such protein families were found (Gollery et al. 2006
). Eight of these families were highly H2O2 responsive but contained only yeast proteins, suggesting that they might be part of a yeast-specific response to H2O2 (data not shown). The 10 remaining protein families had homologs from at least 2 kingdoms and were retained for further analysis. For these 10 unknown protein families, the conservation of the H2O2 induction was restricted to yeast or to yeast and A. thaliana, again demonstrating that the H2O2 response is better conserved between yeast and A. thaliana than between yeast and H. sapiens (table 5).
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The term "protein with unknown function" is used broadly and is mostly based on lack of clear homology with known proteins. A better definition for unknown proteins is "proteins with obscure features" (POFs), which lack defined motifs or protein domains (Gollery et al. 2006
). To identify POFs, the proteins within the different unknown families were subjected to Blast homology searches. In doing so, we were able to identify functional domains and could assign putative functions to 8 out of 10 unknown protein families. One family contained proteins with no functional domains and these are considered to be POFs. A second protein family represented proteins with only predicted membrane function and unknown DUF962 domains. The conserved H2O2 induction of these POFs suggests an important role for them during oxidative stress in yeast or plants. Therefore, these proteins are maybe good candidates to study new aspects of stress signaling and it would be interesting to further analyze the function of these proteins, for example, to improve stress tolerance in these species.
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Conclusions |
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The comparative analysis of H2O2-induced gene expression across kingdoms hints at a strongly specialized transcriptional response, besides a small core eukaryotic H2O2 response. In addition, this analysis clearly reveals that the inductive transcriptional response to H2O2 is highly conserved in yeasts and that this yeast response is more conserved in plants than in animals. Antioxidant gene expression is only induced in unicellular organisms and not in higher eukaryotes, indicating that some specific responses are only partially conserved. Furthermore, the presented approach was used for gene discovery by focusing on unknown proteins, hereby hypothesizing that genes with a conserved H2O2-induced transcription might have an important role during oxidative stress. As more sequence and transcriptome data of other species are expected in the future, sampling within 1 specific kingdom, phylum, or taxon will lead to new insights into the evolution and conservation of the transcriptional response to oxidative stress.
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Acknowledgements |
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The authors thank Francis Dierick and Kenny Billau for creating the Web page containing supplementary data and Dr Martine De Cock for help in preparing the manuscript. This work was supported by a grant from the Research Fund of the Ghent University (Geconcerteerde Onderzoeksacties grant no. 12051403). S.R. is indebted to the "Instituut voor de aanmoediging van Innovatie door Wetenschap en Technologie in Vlaanderen" for a predoctoral fellowship. K.V. is a postdoctoral fellow of the Fund for Scientific Research-Flanders.
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Footnotes |
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Andrew Roger, Associate Editor
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References |
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TOPAbstractIntroductionMaterials and MethodsResults and DiscussionConclusionsAcknowledgementsReferences |
|---|
Abate C, Patel L, Rauscher III FJ, Curran T. Redox regulation of Fos and Jun DNA-binding activity in vitro. Science (1990) 249:1157–1161.
Ahn S-G, Thiele DJ. Redox regulation of mammalian heat shock factor 1 is essential for Hsp gene activation and protection from stress. Genes Dev (2003) 17:516–528.
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 25:3389–3402.
Banzet N, Richaud C, Deveaux Y, Kazmaizer M, Gagnon J, Triantaphylidès C. Accumulation of small heat shock proteins, including mitochondrial HSP22, induced by oxidative stress and adaptive response in tomato cells. Plant J (1998) 13:519–527.[CrossRef][Web of Science][Medline]
Bienert GP, Schjoerring JK, Jahn TP. Membrane transport of hydrogen peroxide. Biochim Biophys Acta (2006) 1758:994–1003.[Medline]
Botella JA, Ulschmid JK, Gruenewald C, Moehle C, Kretzschmar D, Becker K, Schneuwly S. The Drosophila carbonyl reductase sniffer prevents oxidative stress-induced neurodegeneration. Curr Biol (2004) 14:782–786.[CrossRef][Web of Science][Medline]
Chen D, Toone WM, Mata J, Lyne R, Burns G, Kivinen K, Brazma A, Jones N, Bähler J. Global transcriptional responses of fission yeast to environmental stress. Mol Biol Cell (2003) 14:214–229.
Cheng L, Watt R, Piper PW. Polyubiquitin gene expression contributes to oxidative stress resistance in respiratory yeast (Saccharomyces cerevisiae). Mol Gen Genet (1994) 243:358–362.[CrossRef][Medline]
Cheng S-H, Willmann MR, Chen H-C, Sheen J. Calcium signaling through protein kinases. The Arabidopsis calcium-dependent protein kinase gene family. Plant Physiol (2002) 129:469–485.
Chuang Y-YE, Chen Y, Chandramouli GVR, et al, (12 co-authors). Gene expression after treatment with hydrogen peroxide, menadione, or t-butyl hydroperoxide in breast cancer cells. Cancer Res (2002) 62:6246–6254.
Clerch LB. Post-transcriptional regulation of lung antioxidant enzyme gene expression. Ann N Y Acad Sci (2000) 899:103–111.[Web of Science][Medline]
Courgeon AM, Becker J, Maingourd M, Maisonhaute C, Best-Belpomme M. Early activation of heat shock genes in H2O2-treated Drosophila cells. Free Radic Res Commun (1990) 9:147–155.[Medline]
Davletova S, Schlauch K, Coutu J, Mittler R. The zinc-finger protein Zat12 plays a central role in reactive oxygen and abiotic stress signaling in Arabidopsis. Plant Physiol (2005) 139:847–856.
Delauney A, Isnard A-D, Toledano MB. H2O2 sensing through oxidation of the Yap1 transcription factor. EMBO J (2000) 19:5157–5166.[CrossRef][Web of Science][Medline]
Desaint S, Luriau S, Aude J-C, Rousselet G, Toledano MB. Mammalian antioxidant defenses are not inducible by H2O2. J Biol Chem (2004) 279:31157–31163.
Després C, Chubak C, Rochon A, Clark R, Bethune T, Desveaux D, Fobert PR. The Arabidopsis NPR1 disease resistance protein is a novel cofactor that confers redox regulation of DNA binding activity to the basic domain/leucine zipper transcription factor TGA1. Plant Cell (2003) 15:2181–2191.
Donson J, Fang Y, Espiritu-Santo G, Xing W, Salazar A, Miyamoto S, Armendarez V, Volkmuth W. Comprehensive gene expression analysis by transcript profiling. Plant Mol Biol (2002) 48:75–97.[CrossRef][Web of Science][Medline]
Emrich SJ, Barbazuk WB, Li L, Schnable PS. Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res (2007) 17:69–73.
Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res (2002) 30:1575–1584.
Essers MAG, Weijzen S, de Vries-Smits AMM, Saarloos I, de Ruiter ND, Bos JL, Burgering BMT. FOXO transcription factor activation by oxidative stress mediated by the small GTPase Ral and JNK. EMBO J (2004) 23:4802–4812.[CrossRef][Web of Science][Medline]
Finkel T, Holbrook NJ. Oxidants, oxidative stress and the biology of ageing. Nature (2000) 408:239–247.[CrossRef][Medline]
Franklin RA, Rodriguez-Mora OG, LaHair MM, McCubrey JA. Activation of the calcium/calmodulin-dependent protein kinases as a consequence of oxidative stress. Antioxid Redox Signal (2006) 8:1807–1817.[CrossRef][Medline]
Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell (2000) 11:4241–4257.
Georgiou G. How to flip the (redox) switch. Cell (2002) 111:607–610.[CrossRef][Web of Science][Medline]
Girardot F, Monnier V, Tricoire H. Genome wide analysis of common and specific stress responses in adult Drosophila melanogaster. BMC Genomics (2004) 5:74.1–74.16.
Gollery M, Harper J, Cushman J, Mittler T, Girke T, Zhu J-K, Bailey-Serres J, Mittler R. What makes species unique? The contribution of proteins with obscure features. Genome Biol (2006) 7:R57.1–R57.8.
Halliwell B. Reactive species and antioxidants. Redox biology is a fundamental theme of aerobic life. Plant Physiol (2006) 141:312–322.
Härndahl U, Buffoni Hall R, Osteryoung KW, Vierling E, Bornman JF, Sundby C. The chloroplast small heat shock protein undergoes oxidation-dependent conformational changes and may protect plants from oxidative stress. Cell Stress Chaperones (1999) 4:129–138.[CrossRef][Web of Science][Medline]
Hedges SB, Kumar S. Genomic clocks and evolutionary timescales. Trends Genet (2003) 19:200–206.[CrossRef][Web of Science][Medline]
Jakob U, Muse W, Eser M, Bardwell JCA. Chaperone activity with a redox switch. Cell (1999) 96:341–352.[CrossRef][Web of Science][Medline]
Kallberg Y, Oppermann U, Jörnvall H, Persson B. Short-chain dehydrogenase/reductase (SDR) relationships: a large family with eight clusters common to human, animal, and plant genomes. Protein Sci (2002) 11:636–641.[CrossRef][Web of Science][Medline]
Kaminaka H, Näke C, Epple E, et al, (11 co-authors). bZIP10-LSD1 antagonism modulates basal defense and cell death in Arabidopsis following infection. EMBO J (2006) 25:4400–4411.[CrossRef][Web of Science][Medline]
Kim HS, Yu Y, Snesrud EC, Moy LP, Linford LD, Haas BJ, Nierman WC, Quackenbush J. Transcriptional divergence of the duplicated oxidative stress-responsive genes in the Arabidopsis genome. Plant J (2005) 41:212–220.[CrossRef][Web of Science][Medline]
Kobayashi M, Ishizuka T, Katayama M, Kanehisa M, Bhattacharyya-Pakrasi M, Pakrasi HB, Ikeuchi M. Response to oxidative stress involves a novel peroxiredoxin gene in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiol (2004) 45:290–299.
Lee B-H, Won S-H, Lee H-S, Miyao M, Chung W-I, Kim I-Y, Jo J. Expression of the chloroplast-localized small heat shock protein by oxidative stress in rice. Gene (2000) 245:283–290.[CrossRef][Web of Science][Medline]
Lee J-M, Calkins MJ, Chan K, Kan YW, Johnson JA. Identification of the NF-E2-related factor-2-dependent genes conferring protection against oxidative stress in primary cortical astrocytes using oligonucleotide microarray analysis. J Biol Chem (2003) 278:12029–12038.
Li H, Singh AK, McIntyre LM, Sherman LA. Differential gene expression in response to hydrogen peroxide and the putative PerR regulon of Synechocystis sp. strain PCC 6803. J Bacteriol (2004) 186:3331–3345.
Liu H, Colavitti R, Rovira II, Finkel T. Redox-dependent transcriptional regulation. Circ Res (2005) 97:967–974.
Lockhart DJ, Winzeler EA. Genomics, gene expression and DNA arrays. Nature (2000) 405:827–836.[CrossRef][Medline]
Margulis L. Biodiversity: molecular biological domains, symbiosis and kingdom origins. Biosystems (1992) 27:39–51.[CrossRef][Web of Science][Medline]
Matozaki T, Nakanishi H, Takai Y. Small G-protein networks. Their crosstalk and signal cascades. Cell Signal (2000) 12:515–524.[CrossRef][Web of Science][Medline]
Miller G, Mittler R. Could heat shock transcription factors function as hydrogen peroxide sensors in plants? Ann Bot (2006) 98:279–288.
Mittler R, Feng X, Cohen M. Post-transcriptional suppression of cytosolic ascorbate peroxidase expression during pathogen-induced programmed cell death in tobacco. Plant Cell (1998) 10:461–473.
Mittler R, Vanderauwera S, Gollery M, Van Breusegem F. The reactive oxygen gene network in plants. Trends Plant Sci (2004) 9:490–498.[CrossRef][Web of Science][Medline]
Mittler R, Zilinskas BA. Regulation of pea cytosolic ascorbate peroxidase and other antioxidant enzymes during the progression of drought stress and following recovery from drought. Plant J (1994) 5:397–405.[CrossRef][Web of Science][Medline]
Mostertz J, Scharf C, Hecker M, Homuth G. Transcriptome and proteome analysis of Bacillus subtilis gene expression in response to superoxide and peroxide stress. Microbiology (2004) 150:497–512.
Mou Z, Fan W, Dong X. Inducers of plant systemic acquired resistance regulate NPR1 function through redox changes. Cell (2003) 113:935–944.[CrossRef][Web of Science][Medline]
Murray JI, Whitfield ML, Trinklein ND, Myers RM, Brown PO, Botstein D. Diverse and specific gene expression responses to stresses in cultured human cells. Mol Biol Cell (2004) 15:2361–2374.
Neill S, Desikan R, Hancock J. Hydrogen peroxide signalling. Curr Opin Plant Biol (2002) 5:388–395.[CrossRef][Web of Science][Medline]
Neta-Sharir I, Isaacson T, Lurie S, Weiss D. Dual role for tomato heat shock protein 21: protecting photosystem II from oxidative stress and promoting color changes during fruit maturation. Plant Cell (2005) 17:1829–1838.
Pickart CM. Mechanisms underlying ubiquitination. Annu Rev Biochem (2001) 70:503–533.[CrossRef][Web of Science][Medline]
Rentel MC, Lecourieux D, Ouaked F, et al, (11 co-authors). OXI1 kinase is necessary for oxidative burst-mediated signalling in Arabidopsis. Nature (2004) 427:858–861.[CrossRef][Medline]
Rhee SG, Chae HZZ, Kim K. Peroxiredoxins: a historical overview and speculative preview of novel mechanisms and emerging concepts in cell signaling. Free Radic Biol Med (2005) 38:1543–1552.[CrossRef][Web of Science][Medline]
Riechmann JL, Heard J, Martin G, et al, (17 co-authors). Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science (2000) 290:2105–2110.
Rutherford S, Moore I. The Arabidopsis Rab GTPase family: another enigma variation. Curr Opin Plant Biol (2002) 5:518–528.[CrossRef][Web of Science][Medline]
Sauer H, Wartenberg M, Hescheler J. Reactive oxygen species as intracellular messengers during cell growth and differentiation. Cell Physiol Biochem (2001) 11:173–186.[CrossRef][Web of Science][Medline]
Shang F, Gong X, Taylor A. Activity of ubiquitin-dependent pathway in response to oxidative stress. Ubiquitin-activating enzyme is transiently up-regulated. J Biol Chem (1997) 272:23086–23093.
Shang F, Taylor A. Oxidative stress and recovery from oxidative stress are associated with altered ubiquitin conjugating and proteolytic activities in bovine lens epithelial cells. Biochem J (1995) 307:297–303.[Web of Science][Medline]
Shen H-M, Liu Z-G. JNK signaling pathway is a key modulator in cell death mediated by reactive oxygen and nitrogen species. Free Radic Biol Med (2006) 40:928–939.[CrossRef][Web of Science][Medline]
Storz G, Imlay JA. Oxidative stress. Curr Opin Microbiol (1999) 2:188–194.[CrossRef][Web of Science][Medline]
Sunkar R, Kapoor A, Zhu J-K. Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell (2006) 18:2051–2065.
Toone WM, Jones N. Stress-activated signalling pathways in yeast. Genes Cells (1998) 3:485–498.[Abstract]
Touati D. Molecular genetics of superoxide dismutases. Free Radic Biol Med (1988) 5:393–402.[CrossRef][Medline]
Van Breusegem F, Dat JF. Reactive oxygen species in plant cell death. Plant Physiol (2006) 141:384–390.
Vandenabeele S, Van Der Kelen K, Dat J, et al, (12 co-authors). A comprehensive analysis of hydrogen peroxide-induced gene expression in tobacco. Proc Natl Acad Sci USA (2003) 100:16113–16118.
Vanderauwera S, Zimmermann P, Rombauts S, Vandenabeele S, Langebartels C, Gruissem W, Inzé D, Van Breusegem F. Genome-wide analysis of hydrogen peroxide-regulated gene expression in Arabidopsis reveals a high light-induced transcriptional cluster involved in anthocyanin biosynthesis. Plant Physiol (2005) 139:806–821.
Vernoud V, Horton AC, Yang Z, Nielsen E. Analysis of the small GTPase gene superfamily of Arabidopsis. Plant Physiol (2003) 131:1191–1208.
Vivancos AP, Jara M, Zuin A, Sansó M, Hidalgo E. Oxidative stress in Schizosaccharomyces pombe: different H2O2 levels, different response pathways. Mol Genet Genomics (2006) 276:495–502.[CrossRef][Medline]
Volkov RA, Panchuk II, Mullinaux PM, Schöffl F. Heat stress-induced H2O2 is required for effective expression of heat shock genes in Arabidopsis. Plant Mol Biol (2006) 61:733–746.[CrossRef][Web of Science][Medline]
Walsh P, Bursac D, Law YC, Cyr D, Lithgow T. The J-protein family: modulating protein assembly, disassembly and translocation. EMBO Rep (2004) 5:567–571.[CrossRef][Web of Science][Medline]
Wang D, Harper JF, Gribskov M. Systematic trans-genomic comparison of protein kinases between Arabidopsis and Saccharomyces cerevisiae. Plant Physiol (2003) 132:2152–2165.
Wortman JR, Haas BJ, Hannick LI, et al, (12 co-authors). Annotation of the Arabidopsis genome. Plant Physiol (2003) 132:461–468.
Yuan J, Murrell GAC, Trickett A, Landtmeters M, Knoops B, Wang M-X. Overexpression of antioxidant enzyme peroxiredoxin 5 protects human tendon cells against apoptosis and loss of cellular function during oxidative stress. Biochim Biophys Acta (2004) 1693:37–45.[Medline]
Yuan Q, Ouyang S, Liu J, Suh B, Cheung F, Sultana R, Lee D, Quackenbush J, Buell CR. The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res (2003) 31:229–233.
Zámock M, Koller F. Understanding the structure and function of catalases: clues from molecular evolution and in vitro mutagenesis. Prog Biophys Mol Biol (1999) 72:19–66.[CrossRef][Web of Science][Medline]
Zheng M, Wang X, Templeton LJ, Smulski DR, LaRossa RA, Storz G. DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. J Bacteriol (2001) 183:4562–4570.
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