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  • 1
    Electronic Resource
    Electronic Resource
    GENOME TREES AND THE NATURE OF GENOME EVOLUTION (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 59 (2005), S. 191-209 
    Details
    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Genome trees are a means to capture the overwhelming amount of phylogenetic information that is present in genomes. Different formalisms have been introduced to reconstruct genome trees on the basis of various aspects of the genome. On the basis of these aspects, we separate genome trees into five classes: (a) alignment-free trees based on statistic properties of the genome, (b) gene content trees based on the presence and absence of genes, (c) trees based on chromosomal gene order, (d) trees based on average sequence similarity, and (e) phylogenomics-based genome trees. Despite their recent development, genome tree methods have already had some impact on the phylogenetic classification of bacterial species. However, their main impact so far has been on our understanding of the nature of genome evolution and the role of horizontal gene transfer therein. An ideal genome tree method should be capable of using all gene families, including those containing paralogs, in a phylogenomics framework capitalizing on existing methods in conventional phylogenetic reconstruction. We expect such sophisticated methods to help us resolve the branching order between the main bacterial phyla.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.micro.59.030804.121233
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  • 2
    Electronic Resource
    Electronic Resource
    Multiple origins of hydrogenosomes: functional and phylogenetic evidence from the ADP/ATP carrier of the anaerobic chytrid Neocallimastix sp. (2002)
    Oxford, UK : Blackwell Science Ltd
    Molecular microbiology 44 (2002), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: A mitochondrial-type ADP/ATP carrier (AAC) has been identified in the hydrogenosomes of the anaerobic chytridiomycete fungus Neocallimastix sp. L2. Biochemical and immunocytochemical studies revealed that this ADP/ATP carrier is an integral component of hydrogenosomal membranes. Expression of the corresponding cDNA in Escherichia coli confers the ability on the bacterial host to incorporate ADP at significantly higher rates than ATP – similar to isolated mitochondria of yeast and animals. Phylogenetic analysis of this AAC gene (hdgaac) confirmed with high statistical support that the hydrogenosomal ADP/ATP carrier of Neocallimastix sp. L2 belongs to the family of veritable mitochondrial-type AACs. Hydrogenosome-bearing anaerobic ciliates possess clearly distinct mitochondrial-type AACs, whereas the potential hydrogenosomal carrier Hmp31 of the anaerobic flagellate Trichomonas vaginalis and its homologue from Trichomonas gallinae do not belong to this family of proteins. Also, phylogenetic analysis of genes encoding mitochondrial-type chaperonin 60 proteins (HSP 60) supports the conclusion that the hydrogenosomes of anaerobic chytrids and anaerobic ciliates had independent origins, although both of them arose from mitochondria.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.2002.02959.x
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  • 3
    Electronic Resource
    Electronic Resource
    Molecular characterization of phosphoglycerate mutase in archaea (2002)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 212 (2002), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The interconversion of 3-phosphoglycerate and 2-phosphoglycerate during glycolysis and gluconeogenesis is catalyzed by phosphoglycerate mutase (PGM). In bacteria and eukaryotes two structurally distinct enzymes have been found, a cofactor-dependent and a cofactor-independent (iPGM) type. Sequence analysis of archaeal genomes did not find PGMs of either kind, but identified a new family of proteins, distantly related to iPGMs. In this study, these predicted archaeal PGMs from Pyrococcus furiosus and Methanococcus jannaschii have been functionally produced in Escherichia coli, and characterization of the purified proteins has confirmed that they are iPGMs. Analysis of the available microbial genomes indicates that this new type of iPGM is widely distributed among archaea and also encoded in several bacteria. In addition, as has been demonstrated in certain bacteria, some archaea appear to possess an alternative, cofactor-dependent PGM.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.2002.tb11253.x
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  • 4
    Electronic Resource
    Electronic Resource
    The anaerobic chytridiomycete fungus Piromyces sp. E2 produces ethanol via pyruvate:formate lyase and an alcohol dehydrogenase E (2004)
    Oxford, UK : Blackwell Science Ltd
    Molecular microbiology 51 (2004), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Anaerobic chytridiomycete fungi possess hydrogenosomes, which generate hydrogen and ATP, but also acetate and formate as end-products of a prokaryotic-type mixed-acid fermentation. Notably, the anaerobic chytrids Piromyces and Neocallimastix use pyruvate:formate lyase (PFL) for the catabolism of pyruvate, which is in marked contrast to the hydrogenosomal metabolism of the anaerobic parabasalian flagellates Trichomonas vaginalis and Tritrichomonas foetus, because these organisms decarboxylate pyruvate with the aid of pyruvate:ferredoxin oxidoreductase (PFO). Here, we show that the chytrids Piromyces sp. E2 and Neocallimastix sp. L2 also possess an alcohol dehydrogenase E (ADHE) that makes them unique among hydrogenosome-bearing anaerobes. We demonstrate that Piromyces sp. E2 routes the final steps of its carbohydrate catabolism via PFL and ADHE: in axenic culture under standard conditions and in the presence of 0.3% fructose, 35% of the carbohydrates were degraded in the cytosol to the end-products ethanol, formate, lactate and succinate, whereas 65% were degraded via the hydrogenosomes to acetate and formate. These observations require a refinement of the previously published metabolic schemes. In particular, the importance of the hydrogenase in this type of hydrogenosome has to be revisited.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.2003.03912.x
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  • 5
    Electronic Resource
    Electronic Resource
    A divergent ADP/ATP carrier in the hydrogenosomes of Trichomonas gallinae argues for an independent origin of these organelles (2004)
    Oxford, UK : Blackwell Science Ltd
    Molecular microbiology 51 (2004), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: The evolution of mitochondrial ADP and ATP exchanging proteins (AACs) highlights a key event in the evolution of the eukaryotic cell, as ATP exporting carriers were indispensable in establishing the role of mitochondria as ATP-generating cellular organelles. Hydrogenosomes, i.e. ATP- and hydrogen-generating organelles of certain anaerobic unicellular eukaryotes, are believed to have evolved from the same ancestral endosymbiont that gave rise to present day mitochondria. Notably, the hydrogenosomes of the parasitic anaerobic flagellate Trichomonas seemed to be deficient in mitochondrial-type AACs. Instead, HMP 31, a different member of the mitochondrial carrier family (MCF) with a hitherto unknown function, is abundant in the hydrogenosomal membranes of Trichomonas vaginalis. Here we show that the homologous HMP 31 of closely related Trichomonas gallinae specifically transports ADP and ATP with high efficiency, as do genuine mitochondrial AACs. However, phylogenetic analysis and its resistance against bongkrekic acid (BKA, an efficient inhibitor of mitochondrial-type AACs) identify HMP 31 as a member of the mitochondrial carrier family that is distinct from all mitochondrial and hydrogenosomal AACs studied so far. Thus, our data support the hypothesis that the various hydrogenosomes evolved repeatedly and independently.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2958.2004.03918.x
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  • 6
    Electronic Resource
    Electronic Resource
    Equal G and C contents in histone genes indicate selection pressures on mRNA secondary structure (1992)
    Springer
    Journal of molecular evolution 34 (1992), S. 280-291 
    Details
    ISSN: 1432-1432
    Keywords: Histone genes ; Codon usage ; Nucleotide frequencies ; mRNA secondary structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Protein-specific versus taxon-specific patterns of nucleotide frequencies were studied in histone genes. The third positions of codons have a (well-known) taxon-specific G+C level and a histone type-specific G/C ratio. This ratio counterbalances the G/C ratio in the first and second positions so that the overall G and C levels in the coding region become approximately equal. The compensation of the G/C ratio indicates a selection pressure at the mRNA level rather than a selection pressure or mutation bias at the DNA level or a selection pressure on codon usage. The structure of histone mRNAs is compatible with the hypothesis that the G/C compensation is due to selection pressures on mRNA secondary structure. Nevertheless, no specific motifs seem to have been selected, and the free energy of the secondary structures is only slightly lower than that expected on the basis of nucleotide frequencies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00160235
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  • 7
    Electronic Resource
    Electronic Resource
    Exploring Phenotype Space Through Neutral Evolution (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 165-169 
    Details
    ISSN: 1432-1432
    Keywords: Key words: RNA secondary structure — Neutral Evolution — Adaptive evolution — Genotype-phenotype relation — Sequence space — Fitness landscape
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. RNA secondary-structure folding algorithms predict the existence of connected networks of RNA sequences with identical secondary structures. Fitness landscapes that are based on the mapping between RNA sequence and RNA secondary structure hence have many neutral paths. A neutral walk on these fitness landscapes gives access to a virtually unlimited number of secondary structures that are a single point mutation from the neutral path. This shows that neutral evolution explores phenotype space and can play a role in adaptation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006074
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  • 8
    Electronic Resource
    Electronic Resource
    Pattern generation in molecular evolution: Exploitation of the variation in RNA landscapes (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 71-79 
    Details
    ISSN: 1432-1432
    Keywords: RNA secondary structure ; Fitness landscape ; RNA landscape ; Polynucleotide frequency ; Genetic algorithm ; Quasispecies
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Evolution of RNA secondary structure is studied using simulation techniques and statistical analysis of fitness landscapes. The transition from RNA sequence to RNA secondary structure leads to fitness landscapes that have local variations in their “ruggedness.” Evolution exploits these variations. In stable environments it moves the quasispecies toward relatively “flat” peaks, where not only the master sequence but also its mutants have a high fitness. In a rapidly changing environment, the situation is reversed; evolution moves the quasispecies to a region where the correlation between secondary structures of “neighboring” RNA sequences is relatively low. In selection for simple secondary structures the movement toward flat peaks leads to pattern generation in the RNA sequences. Patterns are generated at the level of polynucleotide frequencies and the distribution of purines and pyrimidines. The patterns increase the modularity of the sequence. They thereby prevent the formation of alternative secondary structures after mutations. The movement of the quasispecies toward relatively rugged parts of the landscape results in pattern generation at the level of the RNA secondary structure. The base-pairing frequency of the sequences increases. The patterns that are generated in the RNA sequences and the RNA secondary structures are not directly selected for and can be regarded as a side effect of the evolutionary dynamics of the system.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00178251
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  • 9
    Electronic Resource
    Electronic Resource
    Exploring phenotype space through neutral evolution (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 165-169 
    Details
    ISSN: 1432-1432
    Keywords: RNA secondary structure ; Neutral Evolution ; Adaptive evolution ; Genotype-phenotype relation ; Sequence space ; Fitness landscape
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract RNA secondary-structure folding algorithms predict the existence of connected networks of RNA sequences with identical secondary structures. Fitness landscapes that are based on the mapping between RNA sequence and RNA secondary structure hence have many neutral paths. A neutral walk on these fitness landscapes gives access to a virtually unlimited number of secondary structures that are a single point mutation from the neutral path. This shows that neutral evolution explores phenotype space and can play a role in adaptation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02338823
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  • 10
    Electronic Resource
    Electronic Resource
    Genome phylogeny based on gene content (1999)
    [s.l.] : Nature America Inc.
    Nature genetics 21 (1999), S. 108-110 
    Details
    ISSN: 1546-1718
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Species phylogenies derived from comparisons of single genes are rarely consistent with each other, due to horizontal gene transfer, unrecognized paralogy and highly variable rates of evolution. The advent of completely sequenced genomes allows the construction of a phylogeny that is less ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/5052
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