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  • 1
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    Transcription factor IID in the Archaea: sequences in the Thermococcus celer genome would encode a product closely related to the TATA-binding protein of eukaryotes (1994)
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    Publication Date: 2011-08-24
    Description: The first step in transcription initiation in eukaryotes is mediated by the TATA-binding protein, a subunit of the transcription factor IID complex. We have cloned and sequenced the gene for a presumptive homolog of this eukaryotic protein from Thermococcus celer, a member of the Archaea (formerly archaebacteria). The protein encoded by the archaeal gene is a tandem repeat of a conserved domain, corresponding to the repeated domain in its eukaryotic counterparts. Molecular phylogenetic analyses of the two halves of the repeat are consistent with the duplication occurring before the divergence of the archael and eukaryotic domains. In conjunction with previous observations of similarity in RNA polymerase subunit composition and sequences and the finding of a transcription factor IIB-like sequence in Pyrococcus woesei (a relative of T. celer) it appears that major features of the eukaryotic transcription apparatus were well-established before the origin of eukaryotic cellular organization. The divergence between the two halves of the archael protein is less than that between the halves of the individual eukaryotic sequences, indicating that the average rate of sequence change in the archael protein has been less than in its eukaryotic counterparts. To the extent that this lower rate applies to the genome as a whole, a clearer picture of the early genes (and gene families) that gave rise to present-day genomes is more apt to emerge from the study of sequences from the Archaea than from the corresponding sequences from eukaryotes.
    Keywords: Exobiology
    Type: Proceedings of the National Academy of Sciences of the United States of America (ISSN 0027-8424); Volume 91; 10; 4180-4
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  • 2
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    Ribosomal RNA: a key to phylogeny (1993)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: As molecular phylogeny increasingly shapes our understanding of organismal relationships, no molecule has been applied to more questions than have ribosomal RNAs. We review this role of the rRNAs and some of the insights that have been gained from them. We also offer some of the practical considerations in extracting the phylogenetic information from the sequences. Finally, we stress the importance of comparing results from multiple molecules, both as a method for testing the overall reliability of the organismal phylogeny and as a method for more broadly exploring the history of the genome.
    Keywords: Exobiology
    Type: The FASEB journal : official publication of the Federation of American Societies for Experimental Biology (ISSN 0892-6638); Volume 7; 1; 113-23
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  • 3
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    The Ribosomal Database Project (1992)
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    Publication Date: 2011-08-24
    Description: The Ribosomal Database Project (RDP) complies ribosomal sequences and related data, and redistributes them in aligned and phylogenetically ordered form to its user community. It also offers various software packages for handling, analyzing and displaying sequences. In addition, the RDP offers (or will offer) certain analytic services. At present the project is in an intermediate stage of development.
    Keywords: Exobiology
    Type: Nucleic acids research (ISSN 0305-1048); Volume 20 Suppl; 2199-200
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  • 4
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    Lessons from an Archaeal genome: what are we learning from Methanococcus jannaschii? (1996)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: No abstract available
    Keywords: Exobiology
    Type: Trends in genetics : TIG (ISSN 0168-9525); Volume 12; 10; 377-9
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  • 5
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    Archaeal genomics: an overview (1997)
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    Publication Date: 2011-08-24
    Description: No abstract available
    Keywords: Exobiology
    Type: Cell (ISSN 0092-8674); Volume 89; 7; 991-4
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  • 6
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    A new version of the RDP (Ribosomal Database Project) (1999)
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    Publication Date: 2011-08-24
    Description: The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include 〉9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.
    Keywords: Exobiology
    Type: Nucleic acids research (ISSN 0305-1048); Volume 27; 1; 171-3
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  • 7
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    Methanococcus jannaschii genome: revisited (1996)
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    Publication Date: 2011-08-24
    Description: Analysis of genomic sequences is necessarily an ongoing process. Initial gene assignments tend (wisely) to be on the conservative side (Venter, 1996). The analysis of the genome then grows in an iterative fashion as additional data and more sophisticated algorithms are brought to bear on the data. The present report is an emendation of the original gene list of Methanococcus jannaschii (Bult et al., 1996). By using a somewhat more updated database and more relaxed (and operator-intensive) pattern matching methods, we were able to add significantly to, and in a few cases amend, the gene identification table originally published by Bult et al. (1996).
    Keywords: Exobiology
    Type: Microbial & comparative genomics (ISSN 1090-6592); Volume 1; 4; 329-38
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  • 8
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    An archaeal genomic signature (2000)
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    Publication Date: 2011-08-24
    Description: Comparisons of complete genome sequences allow the most objective and comprehensive descriptions possible of a lineage's evolution. This communication uses the completed genomes from four major euryarchaeal taxa to define a genomic signature for the Euryarchaeota and, by extension, the Archaea as a whole. The signature is defined in terms of the set of protein-encoding genes found in at least two diverse members of the euryarchaeal taxa that function uniquely within the Archaea; most signature proteins have no recognizable bacterial or eukaryal homologs. By this definition, 351 clusters of signature proteins have been identified. Functions of most proteins in this signature set are currently unknown. At least 70% of the clusters that contain proteins from all the euryarchaeal genomes also have crenarchaeal homologs. This conservative set, which appears refractory to horizontal gene transfer to the Bacteria or the Eukarya, would seem to reflect the significant innovations that were unique and fundamental to the archaeal "design fabric." Genomic protein signature analysis methods may be extended to characterize the evolution of any phylogenetically defined lineage. The complete set of protein clusters for the archaeal genomic signature is presented as supplementary material (see the PNAS web site, www.pnas.org).
    Keywords: Exobiology
    Type: Proceedings of the National Academy of Sciences of the United States of America (ISSN 0027-8424); Volume 97; 7; 3304-8
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  • 9
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    An assessment of the impact of radiofrequency interference on microwave SETI searches (1992)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: Investigations are carried out at JPL on radiofrequency interferences at very low levels (-130 to -180 dBm) in various bands, especially the 1-2 GHz band. Extrapolation of interferences in the years to come is attempted.
    Keywords: Exobiology
    Type: Acta astronautica (ISSN 0094-5765); Volume 26; 3-4; 227-32
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  • 10
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    A phylogenetic analysis of Aquifex pyrophilus (1992)
    In:  Other Sources
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    Publication Date: 2019-07-13
    Description: The 16S rRNA of the bacterion Aquifex pyrophilus, a microaerophilic, oxygen-reducing hyperthermophile, has been sequenced directly from the the PCR amplified gene. Phylogenetic analyses show the Aq. pyrophilus lineage to be probably the deepest (earliest) in the (eu)bacterial tree. The addition of this deep branching to the bacterial tree further supports the argument that the Bacteria are of thermophilic ancestry.
    Keywords: Exobiology
    Type: Systematic and applied microbiology (ISSN 0723-2020); 15; 3; 352-6
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