W F Doolittle

..Here, I ask whether this way of thinking is really justified, and explore its implications...

..We also consider evidence for, and implications of, LGT between prokaryotes and phagocytic eukaryotes...

..However, increasing evidence for lateral gene transfer could mean that such attempts are based on an incorrect understanding of evolution...

..The sequence also shows bacteria-like features. It is time to come to grips with this evidence for a mixed heritage...

..However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished...

..The operation of a gene transfer ratchet would inevitably result in the replacement of nuclear genes of early eukaryotes by genes from the bacteria taken by them as food...

..It's not clear that either is the case, but the expanding protist genomic database could help us in several ways...

..We suggest that ribosomal RNA data should be more closely examined with regard to these questions, and we emphasize the importance of developing multiple sequence data sets...

..We discuss these results in light of current views on the origin, evolution, and function of CCT complexes...

..Using concatenated core genes as a valid framework to classify uncharacterized environmental sequences can thus be misleading...

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..Their presence in two divergent archaeal lineages suggests an important adaptive role for these laterally transferred genes...

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..Archaeal family B DNA polymerases together constitute a monophyletic subfamily whose evolution has been characterized by a number of gene duplication events...

..We describe PEG-mediated transformation of H. volcanii WFD11 with intact pHV2 and with a form of pHV2 marked by a 93-base-pair deletion generated in vitro...

..Instead of an organismal tree, we propose that these core genes could be used to define a more subtle and partially reticulated pattern of relationships...

..The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes...

..After an overview of the general sequence features, metabolic pathway studies are explained, using sugar metabolism as an example. The paper closes with an overview of repetitive elements in S. solfataricus...

..The likely effects of deletion and putative displacement ('sliding') of introns on the ability to detect correlations are also examined...

..The nuclear localization signal and negatively charged carboxy-terminus characteristic of eukaryotic pelota-like proteins are absent from the S. solfataricus homolog, and hence may be indicative of the acquired eukaryotic function(s)...

..The persistence of paralogous genes for chaperonin subunits in multiple archaeal lineages may involve a process of co-evolution, where chaperonin subunit heterogeneity changes independently of selection on function...

..Furthermore, reciprocally rooted phylogenies of TrpRS and TyrRS sequences confirm the closer evolutionary relationship of Archaea to eukaryotes by placing the root of the universal tree in the Bacteria...

..It is also consistent with the nearly simultaneous diversification of major eukaryotic lineages implied by the "big-bang" hypothesis of eukaryote evolution...

..In light of recent biochemical and electron microscopic data describing specific CCT-substrate interactions, our results have implications for the evolution of subunit-specific functions in CCT...

..Among these eukaryotic genes are some from deeply branching, amitochondrial eukaryotes (namely Giardia), which further suggests that this event took place quite early in eukaryotic evolution...

..An examination of completely sequenced cosmids suggests a clustering of genes by function in the S. solfataricus genome...

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..The GSI gene of Sulfolobus solfataricus, a member of the Crenarchaeota (extreme thermophiles), is exceptional and could not be definitely placed in either subdivision...

..For hyperthermophiles, we hypothesize that LGT may be as much a consequence as the cause of adaptation to hyperthermophily...

..One horizontal gene exchange might have involved the gram-positive Bacteria and the Archaea, while the other might have occurred between proteobacteria and eukaryotes and might have been mediated by endosymbiosis...

..We propose that several of the incongruencies observed between GAPDH and other molecular phylogenies are artifacts resulting from substitutional saturation of this enzyme...

..This observation suggests that domain 1 contains the codon recognition site, but that the mechanism of eRF1 codon recognition may be more complex than proposed by Nakamura et al. or Knight and Landweber...

..The evolutionary transition from FtsZ to tubulin could provide a window into the transition from prokaryotic cells to eukaryotic cells...

..The phylogenetic diversity of the organisms involved and the range of possible causes and effects of these transfer events make the IPP biosynthetic pathways an ideal system for studying the evolutionary role of LGT...

..Surprisingly, even strains of the same species can differ by as much as 20% in gene content. Conceptual and methodological approaches for dealing with such diversity are now being developed, and should transform microbial genomics...

..Residues involved in feedback inhibition of eubacterial anthranilate synthetases are conserved...

..vaginalis clustered with other eukaryotic ValRS genes, which may have been transferred from the mitochondrial genome to the nuclear genome, suggesting that this amitochondrial trichomonad once harbored an endosymbiotic bacterium...

..With examples from phylogenomics, I argue that "species," "domains," and the "TOL" are reifications that we can do without, especially as genomics dissolves into metagenomics...

..These results indicate that the N.locustae U6 and U2 snRNAs may be functional components of an active spliceosome, even though introns have not yet been found in microsporidian genes...

..The results suggest that sliding, if it occurs at all, has contributed little to the diversity of intron positions...

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..The sequence confirms the distinct nature of crenarchaeotes and provides new insight into the relationships between the three domains: Bacteria, Archaea and Eukaryotes...

..Both Haloarcula vallismortis and Haloarcula hispanica exhibit previously unreported complex life cycles and are therefore significant as genetically approachable models of cellular differentiation within the Archaea...

..The location of a cop homologue upstream of a primase-like gene in pRN1 suggests that it controls DNA replication in a manner similar to these eubacterial plasmids, but does so using a mixture of components from plasmids and viruses...

..The impact of these modular adaptive elements on the cell biology and ecology of S. ruber is substantial, affecting salt adaptation, bioenergetics, and photobiology...

..Few clear examples of recent intron gains have been well documented, but two such cases have now been reported, one with possible identification of the source of the intron...

..Finally, the two most environmentally similar sample sites considered in this study display the greatest overlap of cassette types, consistent with the hypothesis that cassette genes encode adaptive proteins...

..Unlike other HMG-CoA reductases, the enzyme was stable at 90 degrees C and was optimally active at pH 5.5 and 85 degrees C...

..Results of phylogenetic analysis of the coding regions in the putative operon give conflicting evolutionary histories for individual his genes...

..Two of these reading frames are likely related to replication, one encoding a large protein with a helicase domain similar to viral helicases, and the other a copy number control protein, CopG...