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  • 1
    Electronic Resource
    Electronic Resource
    The Core Histone Fold: Limits to Functional Versatility (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 541-542 
    Details
    ISSN: 1432-1432
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02202101
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    The core histone fold: Limits to functional versatility (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 541-542 
    Details
    ISSN: 1432-1432
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02202101
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Conserved Clusters of Functionally Related Genes in Two Bacterial Genomes (1997)
    Springer
    Journal of molecular evolution 44 (1997), S. 66 -73 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Genome analysis — Bacterial evolution — Genome organization — Functional classification — Gene clusters
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. An approach for genome comparison, combining function classification of gene products and sequence comparison, is presented. The genomes of Haemophilus influenzae and Escherichia coli are analyzed, and all genes are classified into nine major functional classes, corresponding to important cellular processes. To study gene order relationships and genome organization in the two bacteria, we performed statistics on neighboring pairs of genes. To estimate the significance of the observations, a statistical model based on binomial distributions has been developed. Significant patterns of gene order are observed within, as well as between, the two bacterial genomes: Functionally related genes tend to be neighbors more often than do unrelated genes. Some of these groups represent well-known operons, but additional gene clusters are identified. These clusters correspond to genomic elements that have been conserved during bacterial evolution. In addition to nearest-neighbor relationships, the method is also useful to study the relative direction of transcription in genomes, which is also highly conserved between homologous gene pairs. This new approach combines the high-level description of molecular function with pair statistics that express genome organization. It is expected to complement traditional methods of sequence analysis in the study of genomic structure, function, and evolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006122
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  • 4
    Electronic Resource
    Electronic Resource
    Nucleic acid-binding metabolic enzymes: Living fossils of stereochemical interactions? (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 564-569 
    Details
    ISSN: 1432-1432
    Keywords: Metabolic enzymes ; Stereochemical interactions ; RNA world
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Recently, a series of intriguing observations expanded the list of a number of metabolic enzymes known to be associated with various forms of nucleic acids, including single- and double-stranded DNA, cognate and noncognate RNAs, and specific tRNAs. There is no clear reason why such a phenomenon should take place in contemporary cell physiology, or, further, why such a property has evolved at all. Sixteen known cases are presented in an attempt to delineate any common features of these enzymes. Apart from their ancient nature, as judged by their wide distribution and their participation in fundamental biochemical pathways, it appears that these enzymes do not share any structural or functional characteristics. Given that most of these proteins require nucleotide-based cofactors for their activity, it is proposed that they may represent genuine molecular fossils of the transition from an RNA to a protein world. Their nucleic acid-binding properties are in keeping with previously proposed hypotheses regarding the origins and evolution of nucleotide-based cofactors. The mode of interaction between these proteins and their nucleic acid substrates remains unclear, but it may represent an extended form of stereochemical interactions that have been proposed for the origins of the genetic code.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00160502
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  • 5
    Electronic Resource
    Electronic Resource
    Universal Protein Families and the Functional Content of the Last Universal Common Ancestor (1999)
    Springer
    Journal of molecular evolution 49 (1999), S. 413-423 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Last Universal Common Ancestor — Cellular evolution — Metabolic reconstruction — Biochemical pathways — Genomics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The phylogenetic distribution of Methanococcus jannaschii proteins can provide, for the first time, an estimate of the genome content of the last common ancestor of the three domains of life. Relying on annotation and comparison with reference to the species distribution of sequence similarities results in 324 proteins forming the universal family set. This set is very well characterized and relatively small and nonredundant, containing 301 biochemical functions, of which 246 are unique. This universal function set contains mostly genes coding for energy metabolism or information processing. It appears that the Last Universal Common Ancestor was an organism with metabolic networks and genetic machinery similar to those of extant unicellular organisms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006564
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  • 6
    Electronic Resource
    Electronic Resource
    A Drosophila hsp70 gene contains long, antiparallel, coupled open reading frames (LAC ORFs) conserved in homologous loci (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 414-420 
    Details
    ISSN: 1432-1432
    Keywords: Gene structure ; Heat shock ; hsp70 ; Antiparallel ORFs ; Drosophila
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A clone isolated from a Drosophila auraria heat-shock cDNA library presents two long, antiparallel, coupled (LAC) open reading frames (ORFs). One strand ORF is 1,929 nucleotides long and exhibits great identity (87.5% at the nucleotide level and 94% at the amino acid level) with the hsp70 gene copies of D. melanogaster, while the second strand ORF, in antiparallel in-frame register arrangement, is 1,839 nucleotides long and exhibits 32% identity with a putative, recently identified, NAD+-dependent glutamate dehydrogenase (NAD+-GDH). The overlap of the two ORFs is 1,824 nucleotides long. Computational analysis shows that this LAC ORF arrangement is conserved in other hsp70 loci in a wide range of organisms, raising questions about possible evolutionary benefits of such a peculiar genomic organization.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00160312
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    Paper (German National Licenses)
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  • 7
    Electronic Resource
    Electronic Resource
    ThiD-TenA: A Gene Pair Fusion in Eukaryotes (1997)
    Springer
    Journal of molecular evolution 45 (1997), S. 708-711 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Gene fusion — ThiD — Function prediction — Transcription — Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Computational analysis of the hypothetical open reading frame MJ0236 from Methanococcus jannaschii reveals its membership to a family of bacterial and eukaryotic proteins, predicted to be the HMP-P kinases involved in thiamin biosyntheis (ThiD). The eukaryotic members of this family contain a C-terminal extension similar to a bacterial transcriptional activator (TenA), thus pointing to a fusion event that took place during cellular evolution. The C-terminal domain is absent from M. jannaschii. The significance of this observation is two-fold: first, this is a case where a fusion protein contains two domains with an unusual phylogenetic distribution, and second, the TenA domain is a rare case of a gene family involved in transcription present both in bacteria and eukaryotes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00013145
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  • 8
    Electronic Resource
    Electronic Resource
    Parallel Origins of the Nucleosome Core and Eukaryotic Transcription from Archaea (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 234-239 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Evolution of transcription — General transcription factors — CCAAT-binding factor subunit — Histones — Archaea — Core Histone fold — Profile searches — Structure prediction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Computational sequence analysis of 10 available archaean histone-like proteins has shown that this family is not only divergently related to the eukaryotic core histones H2A/B, H3, and H4, but also to the central domain of subunits A and C of the CCAAT-binding factor (CBF), a transcription factor associated with eukaryotic promoters. Despite the low sequence identity, it is unambiguously shown that the core histone fold shares a common evolutionary history. Archaean histones and the two CBF families show a remarkable variability in contrast to eukaryotic core histones. Conserved residues shared between families are identified, possibly being responsible for the functional versatility of the core histone fold. The H4 subfamily is most similar to archaean proteins and may be the progenitor of the other core histones in eukaryotes. While it is not clear whether archaean histones are more actively involved in transcription regulation, the present observations link two processes, nucleosomal packing and transcription in a unique way. Both these processes, evidently hybrid in Archaea, have originiated before the ermergence of the eukaryotic cell.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02198849
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  • 9
    Electronic Resource
    Electronic Resource
    Parallel origins of the nucleosome core and eukaryotic transcription from Archaea (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 234-239 
    Details
    ISSN: 1432-1432
    Keywords: Evolution of transcription ; General transcription factors ; CCAAT-binding factor subunit ; Histones ; Archaea ; Core Histone fold ; Profile searches ; Structure prediction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Computational sequence analysis of 10 available archaean histone-like proteins has shown that this family is not only divergently related to the eukaryotic core histones H2A/B, H3, and H4, but also to the central domain of subunits A and C of the CCAAT-binding factor (CBF), a transcription factor associated with eukaryotic promoters. Despite the low sequence identity, it is unambiguously shown that the core histone fold shares a common evolutionary history. Archaean histones and the two CBF families show a remarkable variability in contrast to eukaryotic core histones. Conserved residues shared between families are identified, possibly being responsible for the functional versatility of the core histone fold. The H4 subfamily is most similar to archaean proteins and may be the progenitor of the other core histones in eukaryotes. While it is not clear whether archaean histones are more actively involved in transcription regulation, the present observations link two processes, nucleosomal packing and transcription in a unique way. Both these processes, evidently hybrid in Archaea, have originiated before the ermergence of the eukaryotic cell.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02198849
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    Paper (German National Licenses)
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  • 10
    Electronic Resource
    Electronic Resource
    Protein interaction maps for complete genomes based on gene fusion events (1999)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 402 (1999), S. 86-90 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] A large-scale effort to measure, detect and analyse protein–protein interactions using experimental methods is under way. These include biochemistry such as co-immunoprecipitation or crosslinking, molecular biology such as the two-hybrid system or phage display, and genetics such as ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/47056
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