<?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%">M. A. Huynen</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS Comput Biol</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Computer Simulation DNA Mutational Analysis/methods Evolution *Evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Organelles/physiology Protein Biosynthesis/*genetics Symbiosis/*genetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Fungal Proteins/*physiology Genetic Variation/genetics Humans Mitochondria/*physiology Mitochondrial Proteins/*physiology *Models</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</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=17983265</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">11</style></number><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">e219</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Mitochondria are eukaryotic organelles that originated from the endosymbiosis of an alpha-proteobacterium. To gain insight into the evolution of the mitochondrial proteome as it proceeded through the transition from a free-living cell to a specialized organelle, we compared a reconstructed ancestral proteome of the mitochondrion with the proteomes of alpha-proteobacteria as well as with the mitochondrial proteomes in yeast and man. Overall, there has been a large turnover of the mitochondrial proteome during the evolution of mitochondria. Early in the evolution of the mitochondrion, proteins involved in cell envelope synthesis have virtually disappeared, whereas proteins involved in replication, transcription, cell division, transport, regulation, and signal transduction have been replaced by eukaryotic proteins. More than half of what remains from the mitochondrial ancestor in modern mitochondria corresponds to translation, including post-translational modifications, and to metabolic pathways that are directly, or indirectly, involved in energy conversion. Altogether, the results indicate that the eukaryotic host has hijacked the proto-mitochondrion, taking control of its protein synthesis and metabolism.</style></abstract><notes><style face="normal" font="default" size="100%">Gabaldon, Toni Huynen, Martijn A Research Support, Non-U.S. Gov’t United States PLoS computational biology PLoS Comput Biol. 2007 Nov;3(11):e219. Epub 2007 Sep 26.</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%">Gabaldón, T.</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%">Reconstruction of ancestral proteomes</style></title><secondary-title><style face="normal" font="default" size="100%">Ancestral Sequence Reconstruction</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.us.oup.com/us/catalog/general/subject/LifeSciences/EvolutionaryBiology/?view=usa&amp;ci=9780199299188</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">D. Liberles</style></publisher><pub-location><style face="normal" font="default" size="100%">Oxford</style></pub-location><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%">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%">Boxma, B.</style></author><author><style face="normal" font="default" size="100%">de Graaf, R. M.</style></author><author><style face="normal" font="default" size="100%">van der Staay, G. W.</style></author><author><style face="normal" font="default" size="100%">van Alen, T. A.</style></author><author><style face="normal" font="default" size="100%">Ricard, G.</style></author><author><style face="normal" font="default" size="100%">Gabaldón, T.</style></author><author><style face="normal" font="default" size="100%">van Hoek, A. H.</style></author><author><style face="normal" font="default" size="100%">Moon-van der Staay, S. Y.</style></author><author><style face="normal" font="default" size="100%">Koopman, W. J.</style></author><author><style face="normal" font="default" size="100%">van Hellemond, J. J.</style></author><author><style face="normal" font="default" size="100%">Tielens, A. G.</style></author><author><style face="normal" font="default" size="100%">Friedrich, T.</style></author><author><style face="normal" font="default" size="100%">Veenhuis, M.</style></author><author><style face="normal" font="default" size="100%">M. A. Huynen</style></author><author><style face="normal" font="default" size="100%">Hackstein, J. H.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">An anaerobic mitochondrion that produces hydrogen</style></title><secondary-title><style face="normal" font="default" size="100%">Nature</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">*Anaerobiosis Animals Ciliophora/*cytology/genetics/*metabolism/ultrastructure Cockroaches/parasitology DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Mitochondrial/genetics Electron Transport Electron Transport Complex I/antagonists &amp; inhibitors/metabolism Genome Glucose/metabolism Hydrogen/*metabolism Mitochondria/enzymology/genetics/*metabolism/ultrastructure Molecular Sequence Data Open Reading Fra</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=15744302</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">7029</style></number><volume><style face="normal" font="default" size="100%">434</style></volume><pages><style face="normal" font="default" size="100%">74-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Hydrogenosomes are organelles that produce ATP and hydrogen, and are found in various unrelated eukaryotes, such as anaerobic flagellates, chytridiomycete fungi and ciliates. Although all of these organelles generate hydrogen, the hydrogenosomes from these organisms are structurally and metabolically quite different, just like mitochondria where large differences also exist. These differences have led to a continuing debate about the evolutionary origin of hydrogenosomes. Here we show that the hydrogenosomes of the anaerobic ciliate Nyctotherus ovalis, which thrives in the hindgut of cockroaches, have retained a rudimentary genome encoding components of a mitochondrial electron transport chain. Phylogenetic analyses reveal that those proteins cluster with their homologues from aerobic ciliates. In addition, several nucleus-encoded components of the mitochondrial proteome, such as pyruvate dehydrogenase and complex II, were identified. The N. ovalis hydrogenosome is sensitive to inhibitors of mitochondrial complex I and produces succinate as a major metabolic end product–biochemical traits typical of anaerobic mitochondria. The production of hydrogen, together with the presence of a genome encoding respiratory chain components, and biochemical features characteristic of anaerobic mitochondria, identify the N. ovalis organelle as a missing link between mitochondria and hydrogenosomes.</style></abstract><notes><style face="normal" font="default" size="100%">Boxma, Brigitte de Graaf, Rob M van der Staay, Georg W M van Alen, Theo A Ricard, Guenola Gabaldon, Toni van Hoek, Angela H A M Moon-van der Staay, Seung Yeo Koopman, Werner J H van Hellemond, Jaap J Tielens, Aloysius G M Friedrich, Thorsten Veenhuis, Marten Huynen, Martijn A Hackstein, Johannes H P Research Support, Non-U.S. Gov’t England Nature Nature. 2005 Mar 3;434(7029):74-9.</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%">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%">Gabaldón, T.</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%">Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes</style></title><secondary-title><style face="normal" font="default" size="100%">Bioinformatics</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Animals Chromosome Mapping/*methods DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Mitochondrial/*genetics *Evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular *Gene Deletion Genetic Variation/genetics Humans Linkage Disequilibrium/*genetics Mitochondrial Proteins/*genetics Sequence Homology</style></keyword><keyword><style  face="normal" font="default" size="100%">Nucleic Acid Species Specificity Symbiosis/*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=16204094</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">21 Suppl 2</style></volume><pages><style face="normal" font="default" size="100%">ii144-50</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">MOTIVATION: The endosymbiotic origin of mitochondria has resulted in a massive horizontal transfer of genetic material from an alpha-proteobacterium to the early eukaryotes. Using large-scale phylogenetic analysis we have previously identified 630 orthologous groups of proteins derived from this event. Here we show that this proto-mitochondrial protein set has undergone extensive lineage-specific gene loss in the eukaryotes, with an average of three losses per orthologous group in a phylogeny of nine species. This gene loss has resulted in a high variability of the alphaproteobacterial-derived gene content of present-day eukaryotic genomes that might reflect functional adaptation to different environments. Proteins functioning in the same biochemical pathway tend to have a similar history of gene loss events, and we use this property to predict functional interactions among proteins in our set.</style></abstract><notes><style face="normal" font="default" size="100%">Gabaldon, Toni Huynen, Martijn A Research Support, Non-U.S. Gov’t England Bioinformatics (Oxford, England) Bioinformatics. 2005 Sep 1;21 Suppl 2:ii144-50.</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%">Gabaldón, T.</style></author><author><style face="normal" font="default" size="100%">Rainey, D.</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%">Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I)</style></title><secondary-title><style face="normal" font="default" size="100%">J Mol Biol</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence Animals Computational Biology Electron Transport Complex I/*chemistry/*genetics/metabolism Eukaryotic Cells/*enzymology *Evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Humans Molecular Sequence Data Photosynthesis Phylogeny Plastids/enzymology Protein Binding Protein Subunits/chemistry/genetics/metabolism Sequence Alignment Structural Homology</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein</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=15843018</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">4</style></number><volume><style face="normal" font="default" size="100%">348</style></volume><pages><style face="normal" font="default" size="100%">857-70</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The increasing availability of sequenced genomes enables the reconstruction of the evolutionary history of large protein complexes. Here, we trace the evolution of NADH:ubiquinone oxidoreductase (Complex I), which has increased in size, by so-called supernumary subunits, from 14 subunits in the bacteria to 30 in the plants and algae, 37 in the fungi and 46 in the mammals. Using a combination of pair-wise and profile-based sequence comparisons at the levels of proteins and the DNA of the sequenced eukaryotic genomes, combined with phylogenetic analyses to establish orthology relationships, we were able to (1) trace the origin of six of the supernumerary subunits to the alpha-proteobacterial ancestor of the mitochondria, (2) detect previously unidentified homology relations between subunits from fungi and mammals, (3) detect previously unidentified subunits in the genomes of several species and (4) document several cases of gene duplications among supernumerary subunits in the eukaryotes. One of these, a duplication of N7BM (B17.2), is particularly interesting as it has been lost from genomes that have also lost Complex I proteins, making it a candidate for a Complex I interacting protein. A parsimonious reconstruction of eukaryotic Complex I evolution shows an initial increase in size that predates the separation of plants, fungi and metazoa, followed by a gradual adding and incidental losses of subunits in the various evolutionary lineages. This evolutionary scenario is in contrast to that for Complex I in the prokaryotes, for which the combination of several separate, and previously independently functioning modules into a single complex has been proposed.</style></abstract><notes><style face="normal" font="default" size="100%">Gabaldon, Toni Rainey, Daphne Huynen, Martijn A Research Support, Non-U.S. Gov’t England Journal of molecular biology J Mol Biol. 2005 May 13;348(4):857-70.</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><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%">M. A. Huynen</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Prediction of protein function and pathways in the genome era</style></title><secondary-title><style face="normal" font="default" size="100%">Cell Mol Life Sci</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">ATP-Binding Cassette Transporters/genetics/metabolism Amino Acid Sequence Animals Artificial Gene Fusion Base Sequence Chaperonins/genetics/metabolism Chromosomes/genetics/metabolism Evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular *Genome Genomics Humans Molecular Sequence Data Phylogeny *Proteins/classification/genetics/metabolism RNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Ribosomal/metabolism Sequence Alignment</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</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=15095013</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">7-8</style></number><volume><style face="normal" font="default" size="100%">61</style></volume><pages><style face="normal" font="default" size="100%">930-44</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The growing number of completely sequenced genomes adds new dimensions to the use of sequence analysis to predict protein function. Compared with the classical knowledge transfer from one protein to a similar sequence (homology-based function prediction), knowledge about the corresponding genes in other genomes (orthology-based function prediction) provides more specific information about the protein’s function, while the analysis of the sequence in its genomic context (context-based function prediction) provides information about its functional context. Whereas homology-based methods predict the molecular function of a protein, genomic context methods predict the biological process in which it plays a role. These complementary approaches can be combined to elucidate complete functional networks and biochemical pathways from the genome sequence of an organism. Here we review recent advances in the field of genomic-context based methods of protein function prediction. Techniques are highlighted with examples, including an analysis that combines information from genomic-context with homology to predict a role of the RNase L inhibitor in the maturation of ribosomal RNA.</style></abstract><notes><style face="normal" font="default" size="100%">Gabaldon, T Huynen, M A Review Switzerland Cellular and molecular life sciences : CMLS Cell Mol Life Sci. 2004 Apr;61(7-8):930-44.</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%">Gabaldón, T.</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%">Shaping the mitochondrial proteome</style></title><secondary-title><style face="normal" font="default" size="100%">Biochim Biophys Acta</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Animals Biological Transport Energy Metabolism Eukaryotic Cells/physiology *Evolution Humans Mitochondria/*physiology Phylogeny Proteome/*physiology</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</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=15576054</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">2-3</style></number><volume><style face="normal" font="default" size="100%">1659</style></volume><pages><style face="normal" font="default" size="100%">212-20</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Mitochondria are eukaryotic organelles that originated from a single bacterial endosymbiosis some 2 billion years ago. The transition from the ancestral endosymbiont to the modern mitochondrion has been accompanied by major changes in its protein content, the so-called proteome. These changes included complete loss of some bacterial pathways, amelioration of others and gain of completely new complexes of eukaryotic origin such as the ATP/ADP translocase and most of the mitochondrial protein import machinery. This renewal of proteins has been so extensive that only 14-16% of modern mitochondrial proteome has an origin that can be traced back to the bacterial endosymbiont. The rest consists of proteins of diverse origin that were eventually recruited to function in the organelle. This shaping of the proteome content reflects the transformation of mitochondria into a highly specialized organelle that, besides ATP production, comprises a variety of functions within the eukaryotic metabolism. Here we review recent advances in the fields of comparative genomics and proteomics that are throwing light on the origin and evolution of the mitochondrial proteome.</style></abstract><notes><style face="normal" font="default" size="100%">Gabaldon, Toni Huynen, Martijn A Research Support, Non-U.S. Gov’t Review Netherlands Biochimica et biophysica acta Biochim Biophys Acta. 2004 Dec 6;1659(2-3):212-20.</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%">Gabaldón, T.</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%">Reconstruction of the proto-mitochondrial metabolism</style></title><secondary-title><style face="normal" font="default" size="100%">Science</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Aerobiosis Algorithms Alphaproteobacteria/chemistry/genetics/*metabolism Amino Acids/metabolism Animals Bacterial Proteins/chemistry/*metabolism Genome Genome</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Glycerol/metabolism Humans Lipid Metabolism Mitochondria/chemistry/genetics/*metabolism Phylogeny *Proteome Symbiosis Yeasts/metabolism</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</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=12893934</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">5633</style></number><volume><style face="normal" font="default" size="100%">301</style></volume><pages><style face="normal" font="default" size="100%">609</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><notes><style face="normal" font="default" size="100%">Gabaldon, Toni Huynen, Martijn A Comparative Study Research Support, Non-U.S. Gov’t United States Science (New York, N.Y.) Science. 2003 Aug 1;301(5633):609.</style></notes></record></records></xml>