<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gabaldón, T.</style></author><author><style face="normal" font="default" size="100%">B. Snel</style></author><author><style face="normal" font="default" size="100%">van Zimmeren, F.</style></author><author><style face="normal" font="default" size="100%">Hemrika, W.</style></author><author><style face="normal" font="default" size="100%">Tabak, H.</style></author><author><style face="normal" font="default" size="100%">M. A. Huynen</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Origin and evolution of the peroxisomal proteome</style></title><secondary-title><style face="normal" font="default" size="100%">Biol Direct</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2006</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=16556314</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">1</style></volume><pages><style face="normal" font="default" size="100%">8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Peroxisomes are ubiquitous eukaryotic organelles involved in various oxidative reactions. Their enzymatic content varies between species, but the presence of common protein import and organelle biogenesis systems support a single evolutionary origin. The precise scenario for this origin remains however to be established. The ability of peroxisomes to divide and import proteins post-translationally, just like mitochondria and chloroplasts, supports an endosymbiotic origin. However, this view has been challenged by recent discoveries that mutant, peroxisome-less cells restore peroxisomes upon introduction of the wild-type gene, and that peroxisomes are formed from the Endoplasmic Reticulum. The lack of a peroxisomal genome precludes the use of classical analyses, as those performed with mitochondria or chloroplasts, to settle the debate. We therefore conducted large-scale phylogenetic analyses of the yeast and rat peroxisomal proteomes. RESULTS : Our results show that most peroxisomal proteins (39-58%) are of eukaryotic origin, comprising all proteins involved in organelle biogenesis or maintenance. A significant fraction (13-18%), consisting mainly of enzymes, has an alpha-proteobacterial origin and appears to be the result of the recruitment of proteins originally targeted to mitochondria. Consistent with the findings that peroxisomes are formed in the Endoplasmic Reticulum, we find that the most universally conserved Peroxisome biogenesis and maintenance proteins are homologous to proteins from the Endoplasmic Reticulum Assisted Decay pathway. CONCLUSION: Altogether our results indicate that the peroxisome does not have an endosymbiotic origin and that its proteins were recruited from pools existing within the primitive eukaryote. Moreover the reconstruction of primitive peroxisomal proteomes suggests that ontogenetically as well as phylogenetically, peroxisomes stem from the Endoplasmic Reticulum. REVIEWERS: This article was reviewed by Arcady Mushegian, Gaspar Jekely and John Logsdon. OPEN PEER REVIEW: Reviewed by Arcady Mushegian, Gaspar Jekely and John Logsdon. For the full reviews, please go to the Reviewers’ comments section.</style></abstract><notes><style face="normal" font="default" size="100%">Gabaldon, Toni Snel, Berend van Zimmeren, Frank Hemrika, Wieger Tabak, Henk Huynen, Martijn A England Biology direct Biol Direct. 2006 Mar 23;1:8.</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>5</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">M. A. Huynen</style></author><author><style face="normal" font="default" size="100%">B. Snel</style></author><author><style face="normal" font="default" size="100%">Gabaldón T</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Reliable and specific protein function prediction by combining homology with genomic(s) context</style></title><secondary-title><style face="normal" font="default" size="100%">Discovery of biomolecular mechanisms with theoretical data analyses</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2006</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.landesbioscience.com/iu/output.php?id=479</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">F. Eisenhaber, Landes Bioscience</style></publisher><language><style face="normal" font="default" size="100%">eng</style></language></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">M. A. Huynen</style></author><author><style face="normal" font="default" size="100%">Spronk, C. A.</style></author><author><style face="normal" font="default" size="100%">Gabaldón, T.</style></author><author><style face="normal" font="default" size="100%">B. Snel</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin</style></title><secondary-title><style face="normal" font="default" size="100%">FEBS Lett</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">*Genome Glutaredoxins Models</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Oxidoreductases/chemistry/*metabolism Phylogeny Protein Conformation</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=15670813</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">3</style></number><volume><style face="normal" font="default" size="100%">579</style></volume><pages><style face="normal" font="default" size="100%">591-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Genomes, functional genomics data and 3D structure reflect different aspects of protein function. Here, we combine these data to predict that BolA, a widely distributed protein family with unknown function, is a reductase that interacts with a glutaredoxin. Comparisons at the 3D structure level as well as at the sequence profile level indicate homology between BolA and OsmC, an enzyme that reduces organic peroxides. Complementary to this, comparative analyses of genomes and genomics data provide strong evidence of an interaction between BolA and the mono-thiol glutaredoxin family. The interaction between BolA and a mono-thiol glutaredoxin is of particular interest because BolA does not, in contrast to its homolog OsmC, have evolutionarily conserved cysteines to provide it with reducing equivalents. We propose that BolA uses the mono-thiol glutaredoxin as the source for these.</style></abstract><notes><style face="normal" font="default" size="100%">Huynen, Martijn A Spronk, Chris A E M Gabaldon, Toni Snel, Berend Research Support, Non-U.S. Gov’t Netherlands FEBS letters FEBS Lett. 2005 Jan 31;579(3):591-6.</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">M. A. Huynen</style></author><author><style face="normal" font="default" size="100%">Gabaldón, T.</style></author><author><style face="normal" font="default" size="100%">B. Snel</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Variation and evolution of biomolecular systems: searching for functional relevance</style></title><secondary-title><style face="normal" font="default" size="100%">FEBS Lett</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">*Evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Genetic Variation Multiprotein Complexes/*genetics Phylogeny Protein Binding/genetics</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=15763561</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">8</style></number><volume><style face="normal" font="default" size="100%">579</style></volume><pages><style face="normal" font="default" size="100%">1839-45</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The availability of genome sequences and functional genomics data from multiple species enables us to compare the composition of biomolecular systems like biochemical pathways and protein complexes between species. Here, we review small- and large-scale, &quot;genomics-based&quot; approaches to biomolecular systems variation. In general, caution is required when comparing the results of bioinformatics analyses of genomes or of functional genomics data between species. Limitations to the sensitivity of sequence analysis tools and the noisy nature of genomics data tend to lead to systematic overestimates of the amount of variation. Nevertheless, the results from detailed manual analyses, and of large-scale analyses that filter out systematic biases, point to a large amount of variation in the composition of biomolecular systems. Such observations challenge our understanding of the function of the systems and their individual components and can potentially facilitate the identification and functional characterization of sub-systems within a system. Mapping the inter-species variation of complex biomolecular systems on a phylogenetic species tree allows one to reconstruct their evolution.</style></abstract><notes><style face="normal" font="default" size="100%">Huynen, Martijn A Gabaldon, Toni Snel, Berend Review Netherlands FEBS letters FEBS Lett. 2005 Mar 21;579(8):1839-45.</style></notes></record></records></xml>