Hydrogen peroxide-induced gene expression across kingdoms: a comparative analysis.


: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 (H(2)O(2))-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 H(2)O(2)-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 H(2)O(2) responsive across kingdoms: DNAJ domain-containing heat shock proteins, small guanine triphosphate-binding proteins, Ca(2+)-dependent protein kinases, and ubiquitin-conjugating enzymes.


Mol Biol Evol


Vandenbroucke K,Robbens S,Vandepoele K,Inzé D,Van de Peer Y,Van Breusegem F




Has Abstract


2008-03-01 00:00:00














  • Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication.

    abstract::Insertions and deletions (indels) in protein-coding genes are important sources of genetic variation. Their role in creating new proteins may be especially important after gene duplication. However, little is known about how indels affect the divergence of duplicate genes. We here study thousands of duplicate genes in...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Guo B,Zou M,Wagner A

    更新日期:2012-10-01 00:00:00

  • The number of alleles at a microsatellite defines the allele frequency spectrum and facilitates fast accurate estimation of theta.

    abstract::Theoretical work focused on microsatellite variation has produced a number of important results, including the expected distribution of repeat sizes and the expected squared difference in repeat size between two randomly selected samples. However, closed-form expressions for the sampling distribution and frequency spe...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Haasl RJ,Payseur BA

    更新日期:2010-12-01 00:00:00

  • Mutational and Selective Processes Involved in Evolution during Bacterial Range Expansions.

    abstract::Bacterial populations have been shown to accumulate deleterious mutations during spatial expansions that overall decrease their fitness and ability to grow. However, it is unclear if and how they can respond to selection in face of this mutation load. We examine here if artificial selection can counteract the negative...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Bosshard L,Peischl S,Ackermann M,Excoffier L

    更新日期:2019-10-01 00:00:00

  • Molecular Biology and Evolution of Cancer: From Discovery to Action.

    abstract::Cancer progression is an evolutionary process. During this process, evolving cancer cell populations encounter restrictive ecological niches within the body, such as the primary tumor, circulatory system, and diverse metastatic sites. Efforts to prevent or delay cancer evolution-and progression-require a deep understa...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Somarelli JA,Gardner H,Cannataro VL,Gunady EF,Boddy AM,Johnson NA,Fisk JN,Gaffney SG,Chuang JH,Li S,Ciccarelli FD,Panchenko AR,Megquier K,Kumar S,Dornburg A,DeGregori J,Townsend JP

    更新日期:2020-02-01 00:00:00

  • Ecological nitrogen limitation shapes the DNA composition of plant genomes.

    abstract::Phenotypes and behaviors respond to resource constraints via adaptation, but the influence of ecological limitations on the composition of eukaryotic genomes is still unclear. We trace connections between plant ecology and genomes through their elemental composition. Inorganic sources of nitrogen (N) are severely limi...

    journal_title:Molecular biology and evolution

    pub_type: 信件


    authors: Acquisti C,Elser JJ,Kumar S

    更新日期:2009-05-01 00:00:00

  • Organellar RNA editing and plant-specific extensions of pentatricopeptide repeat proteins in jungermanniid but not in marchantiid liverworts.

    abstract::The pyrimidine exchange type of RNA editing in land plant (embryophyte) organelles has largely remained an enigma with respect to its biochemical mechanisms, the underlying specificities, and its raison d'être. Apparently arising with the earliest embryophytes, RNA editing is conspicuously absent in one clade of liver...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Rüdinger M,Polsakiewicz M,Knoop V

    更新日期:2008-07-01 00:00:00

  • Molecular evolution of the period gene in Drosophila athabasca.

    abstract::We measured nucleotide variability within and between the three semispecies of the Drosophila athabasca complex, at the period (per) gene by using a polymerase chain reaction-based four-cutter restriction-enzyme analysis. The levels of polymorphism varied considerably between the three semispecies. Our results for per...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Ford MJ,Yoon CK,Aquadro CF

    更新日期:1994-03-01 00:00:00

  • Evolutionary relationships of class II major-histocompatibility-complex genes in mammals.

    abstract::The major histocompatibility complex (MHC) class II molecule consists of noncovalently associated alpha and beta chains. In mammals studied so far, the class II MHC can be divided into a number of regions, each containing one or more alpha-chain genes (A genes) and beta-chain genes (B genes), and it has been known for...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Hughes AL,Nei M

    更新日期:1990-11-01 00:00:00

  • Sequential evolution of a symbiont inferred from the host: Wolbachia and Drosophila simulans.

    abstract::This study aims to unravel the biogeography of a model symbiont/host system by exploiting the prediction that a symbiont will leave a signature of infection on the host. Specifically, a global sample of 1,442 Drosophila simulans from 33 countries and 64 sampling localities was employed to infer the phylogeography of t...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Ballard JW

    更新日期:2004-03-01 00:00:00

  • Demosponge EST sequencing reveals a complex genetic toolkit of the simplest metazoans.

    abstract::Sponges (Porifera) are among the simplest living and the earliest branching metazoans. They hold a pivotal role for studying genome evolution of the entire metazoan branch, both as an outgroup to Eumetazoa and as the closest branching phylum to the common ancestor of all multicellular animals (Urmetazoa). In order to ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Harcet M,Roller M,Cetković H,Perina D,Wiens M,Müller WE,Vlahovicek K

    更新日期:2010-12-01 00:00:00

  • Life History of the Oldest Lentivirus: Characterization of ELVgv Integrations in the Dermopteran Genome.

    abstract::Endogenous retroviruses are genomic elements formed by germline infiltration by originally exogenous viruses. These molecular fossils provide valuable information about the evolution of the retroviral family. Lentiviruses are an extensively studied genus of retroviruses infecting a broad range of mammals. Despite a we...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Hron T,Farkašová H,Padhi A,Pačes J,Elleder D

    更新日期:2016-10-01 00:00:00

  • Molecular Diversification of the Seminal Fluid Proteome in a Recently Diverged Passerine Species Pair.

    abstract::Seminal fluid proteins (SFPs) mediate an array of postmating reproductive processes that influence fertilization and fertility. As such, it is widely held that SFPs may contribute to postmating, prezygotic reproductive barriers between closely related taxa. We investigated seminal fluid (SF) diversification in a recen...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Rowe M,Whittington E,Borziak K,Ravinet M,Eroukhmanoff F,Sætre GP,Dorus S

    更新日期:2020-02-01 00:00:00

  • Possible horizontal transfer of a transposable element from host to parasitoid.

    abstract::Full-length mariner-like elements (MLEs) were identified from both a parasitoid wasp, Ascogaster reticulatus, and its moth host, Adoxophyes honmai. MLEs were detected in two related Tortricid moths, but not in another Ascogaster species. The MLEs of A. reticulatus and A. honmai were 97.6% identical in DNA sequence. Th...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Yoshiyama M,Tu Z,Kainoh Y,Honda H,Shono T,Kimura K

    更新日期:2001-10-01 00:00:00

  • Deletion rate evolution and its effect on genome size and coding density.

    abstract::Deletion rates are thought to be important factors in determining the genome size of organisms in nature. Although it is indisputable that deletions, and thus deletion rates, affect genome size, it is unclear how, or indeed if, genome size is regulated via the deletion rate. Here, we employ a mathematical model to det...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Pettersson ME,Kurland CG,Berg OG

    更新日期:2009-06-01 00:00:00

  • Natural selection and the molecular clock.

    abstract::This paper concludes that the statistical properties of protein evolution are compatible with a particular model of evolution by natural selection. The argument begins with a statistical description of the molecular clock based on a Poisson process with a randomly varying tick rate. If the time scale of the change of ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Gillespie JH

    更新日期:1986-03-01 00:00:00

  • An analysis of determinants of amino acids substitution rates in bacterial proteins.

    abstract::The variation of amino acid substitution rates in proteins depends on several variables. Among these, the protein's expression level, functional category, essentiality, or metabolic costs of its amino acid residues may play an important role. However, the relative importance of each variable has not yet been evaluated...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Rocha EP,Danchin A

    更新日期:2004-01-01 00:00:00

  • How Long Does Wolbachia Remain on Board?

    abstract::Wolbachia bacteria infect about half of all arthropods, with diverse and extreme consequences ranging from sex-ratio distortion and mating incompatibilities to protection against viruses. These phenotypic effects, combined with efficient vertical transmission from mothers to offspring, satisfactorily explain the invas...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Bailly-Bechet M,Martins-Simões P,Szöllosi GJ,Mialdea G,Sagot MF,Charlat S

    更新日期:2017-05-01 00:00:00

  • Origin and Evolution of Water Oxidation before the Last Common Ancestor of the Cyanobacteria.

    abstract::Photosystem II, the water oxidizing enzyme, altered the course of evolution by filling the atmosphere with oxygen. Here, we reconstruct the origin and evolution of water oxidation at an unprecedented level of detail by studying the phylogeny of all D1 subunits, the main protein coordinating the water oxidizing cluster...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Cardona T,Murray JW,Rutherford AW

    更新日期:2015-05-01 00:00:00

  • ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy.

    abstract::Phylogenetic inference from genome-wide data (phylogenomics) has revolutionized the study of evolution because it enables accounting for discordance among evolutionary histories across the genome. To this end, summary methods have been developed to allow accurate and scalable inference of species trees from gene trees...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Zhang C,Scornavacca C,Molloy EK,Mirarab S

    更新日期:2020-11-01 00:00:00

  • DNA-DNA hybridization evidence of the rapid rate of muroid rodent DNA evolution.

    abstract::Single-copy nuclear DNAs (scnDNAs) of eight species of arvicoline and six species of murine rodents were compared using DNA-DNA hybridization. The branching pattern derived from the DNA comparisons is congruent with the fossil evidence and supported by comparative biochemical, chromosomal, and morphological studies. T...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Catzeflis FM,Sheldon FH,Ahlquist JE,Sibley CG

    更新日期:1987-05-01 00:00:00

  • Evolution of paralogous genes: Reconstruction of genome rearrangements through comparison of multiple genomes within Staphylococcus aureus.

    abstract::Analysis of evolution of paralogous genes in a genome is central to our understanding of genome evolution. Comparison of closely related bacterial genomes, which has provided clues as to how genome sequences evolve under natural conditions, would help in such an analysis. With species Staphylococcus aureus, whole-geno...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Tsuru T,Kawai M,Mizutani-Ui Y,Uchiyama I,Kobayashi I

    更新日期:2006-06-01 00:00:00

  • The increase in the number of subunits in eukaryotic RNA polymerase III relative to RNA polymerase II is due to the permanent recruitment of general transcription factors.

    abstract::The number of subunits of RNA polymerases (RNAPs) increases during evolution from 5 in eubacteria to 12 in archaea. In eukaryotes, which have at least three RNAPs, the number of subunits has expanded from 12 in RNA polymerase II (RNAPII) to 14 in RNA polymerase I (RNAPI) and to 17 in RNA polymerase III (RNAPIII). It w...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Carter R,Drouin G

    更新日期:2010-05-01 00:00:00

  • Human long noncoding RNAs are substantially less folded than messenger RNAs.

    abstract::Long noncoding RNAs (lncRNAs) do not code for proteins but function as RNAs. Because the functions of an RNA rely on either its sequence or secondary structure, lncRNAs should be folded at least as strongly as messenger RNAs (mRNAs), which serve as messengers for translation and are generally thought to lack secondary...

    journal_title:Molecular biology and evolution

    pub_type: 信件


    authors: Yang JR,Zhang J

    更新日期:2015-04-01 00:00:00

  • SPIn: model selection for phylogenetic mixtures via linear invariants.

    abstract::In phylogenetic inference, an evolutionary model describes the substitution processes along each edge of a phylogenetic tree. Misspecification of the model has important implications for the analysis of phylogenetic data. Conventionally, however, the selection of a suitable evolutionary model is based on heuristics or...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Kedzierska AM,Drton M,Guigó R,Casanellas M

    更新日期:2012-03-01 00:00:00

  • Evolutionary transfer of ORF-containing group I introns between different subcellular compartments (chloroplast and mitochondrion).

    abstract::We describe here a case of homologous introns containing homologous open reading frames (ORFs) that are inserted at the same site in the large subunit (LSU) rRNA gene of different organelles in distantly related organisms. We show that the chloroplast LSU rRNA gene of the green alga Chlamydomonas pallidostigmatica con...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Turmel M,Côté V,Otis C,Mercier JP,Gray MW,Lonergan KM,Lemieux C

    更新日期:1995-07-01 00:00:00

  • Evolutionary origins of human herpes simplex viruses 1 and 2.

    abstract::Herpesviruses have been infecting and codiverging with their vertebrate hosts for hundreds of millions of years. The primate simplex viruses exemplify this pattern of virus-host codivergence, at a minimum, as far back as the most recent common ancestor of New World monkeys, Old World monkeys, and apes. Humans are the ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Wertheim JO,Smith MD,Smith DM,Scheffler K,Kosakovsky Pond SL

    更新日期:2014-09-01 00:00:00

  • Molecular distance and divergence time in carnivores and primates.

    abstract::Numerous studies have used indices of genetic distance between species to reconstruct evolutionary relationships and to estimate divergence time. However, the empirical relationship between molecular-based indices of genetic divergence and divergence time based on the fossil record is poorly known. To date, the result...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Wayne RK,Van Valkenburgh B,O'Brien SJ

    更新日期:1991-05-01 00:00:00

  • Molecular evolution of the primate developmental genes MSX1 and PAX9.

    abstract::In primates, the craniofacial skeleton and the dentition are marked by high levels of interspecific variation. Despite this, there are few comparative species studies conducted at the molecular level to investigate this functional diversity. We have determined nucleotide sequences of MSX1 and PAX9, two developmental g...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Perry GH,Verrelli BC,Stone AC

    更新日期:2006-03-01 00:00:00

  • The "domino theory" of gene death: gradual and mass gene extinction events in three lineages of obligate symbiotic bacterial pathogens.

    abstract::During the adaptation of an organism to a parasitic lifestyle, various gene functions may be rendered superfluous due to the fact that the host may supply these needs. As a consequence, obligate symbiotic bacterial pathogens tend to undergo reductive genomic evolution through gene death (nonfunctionalization or pseudo...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Dagan T,Blekhman R,Graur D

    更新日期:2006-02-01 00:00:00

  • Homologs of mitochondrial transcription factor B, sparsely distributed within the eukaryotic radiation, are likely derived from the dimethyladenosine methyltransferase of the mitochondrial endosymbiont.

    abstract::Mitochondrial transcription factor B (mtTFB), an essential component in regulating the expression of mitochondrial DNA-encoded genes in both yeast and humans, is a dimethyladenosine methyltransferase (DMT) that has acquired a secondary role in mitochondrial transcription. So far, mtTFB has only been well studied in Op...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Shutt TE,Gray MW

    更新日期:2006-06-01 00:00:00