| 1. |
- Harish, Ajith, et al.
(author)
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Rooted phylogeny of the three superkingdoms.
- 2013
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In: Biochimie. - : Elsevier BV. - 1638-6183 .- 0300-9084. ; 95:8, s. 1593-1604
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Journal article (peer-reviewed)abstract
- The traditional bacterial rooting of the three superkingdoms in sequence-based gene trees is inconsistent with new phylogenetic reconstructions based on genome content of compact protein domains. We find that protein domains at the level of the SCOP superfamily (SF) from sequenced genomes implement with maximum parsimony fully resolved rooted trees. Such genome content trees identify archaea and bacteria (akaryotes) as sister clades that diverge from an akaryote common ancestor, LACA. Several eukaryote sister clades diverge from a eukaryote common ancestor, LECA. LACA and LECA descend in parallel from the most recent universal common ancestor (MRUCA), which is not a bacterium. Rather, MRUCA presents 75% of the unique SFs encoded by extant genomes of the three superkingdoms, each encoding a proteome that partially overlaps all others. This alone implies that the common ancestor to the superkingdoms was very complex. Such ancestral complexity is confirmed by phylogenetic reconstructions. In addition, the divergence of proteomes from the complex ancestor in each superkingdom is both reductive in numbers of unique SFs as well as cumulative in the abundance of surviving SFs. These data suggest that the common ancestor was not the first cell lineage and that modern global phylogeny is the crown of a "recently" re-rooted tree. We suggest that a bottlenecked survivor of an environmental collapse, which preceded the flourishing of the modern crown, seeded the current phylogenetic tree.
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| 2. |
- Kurland, Charles
(author)
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Carl R. Woese in memoriam Obituary
- 2013
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In: Biochimie. - : Elsevier BV. - 1638-6183 .- 0300-9084. ; 95:9, s. 1661-1662
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Journal article (other academic/artistic)
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| 3. |
- Kurland, Charles
(author)
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The RNA dreamtime: modern cells feature proteins that might have supported a prebiotic polypeptide world but nothing indicates that RNA world ever was.
- 2010
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In: BioEssays. - : Wiley. - 0265-9247. ; 32:10, s. 866-871
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Journal article (peer-reviewed)abstract
- Modern cells present no signs of a putative prebiotic RNA world. However, RNA coding is not a sine qua non for the accumulation of catalytic polypeptides. Thus, cellular proteins spontaneously fold into active structures that are resistant to proteolysis. The law of mass action suggests that binding domains are stabilized by specific interactions with their substrates. Random polypeptide synthesis in a prebiotic world has the potential to initially produce only a very small fraction of polypeptides that can fold spontaneously into catalytic domains. However, that fraction can be enriched by proteolytic activities that destroy the unfolded polypeptides and regenerate amino acids that can be recycled into polypeptides. In this open system scenario the stable domains that accumulate and the chemical environment in which they are accumulated are linked through self coding of polypeptide structure. Such open polypeptide systems may have been the precursors to the cellular ribonucleoprotein (RNP) world that evolved subsequently.
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| 4. |
- Lind, Peter A, et al.
(author)
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Compensatory gene amplification restores fitness after inter-species gene replacements
- 2010
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In: Molecular Microbiology. - : Wiley. - 0950-382X .- 1365-2958. ; 75:5, s. 1078-1089
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Journal article (peer-reviewed)abstract
- Genes introduced by gene replacements and other types of horizontal gene transfer (HGT) represent a significant presence in many archaeal and eubacterial genomes. Most alien genes are likely to be neutral or deleterious upon arrival and their long-term persistence may require a mechanism that improves their selective contribution. To examine the fate of inter-species gene replacements, we exchanged three native S. typhimurium genes encoding ribosomal proteins with orthologues from various other microbes. The results show that replacement of each of these three genes reduces fitness to such an extent that it would provide an effective barrier against inter-species gene replacements in eubacterial populations. However, these fitness defects could be partially ameliorated by gene amplification that augmented the dosage of the heterologous proteins. This suggests that suboptimal expression is a common fitness constraint for inter-species gene replacements, with fitness costs conferred by either a lower expression level of the alien protein compared with the native protein or a requirement for an increased amount of the alien protein to maintain proper function. Our findings can explain the observation that duplicated genes are over-represented among horizontally transferred genes, and suggest a potential coupling between compensatory gene amplification after HGT and the evolution of new genes.
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| 5. |
- Wang, Minglei, et al.
(author)
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Reductive evolution of proteomes and protein structures
- 2011
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In: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 108:29, s. 11954-11958
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Journal article (peer-reviewed)abstract
- The lengths of orthologous protein families in Eukarya are almost double the lengths found in Bacteria and Archaea. Here we examine protein structures in 745 genomes and show that protein length differences between superkingdoms arise as much shorter prokaryotic nondomain linker sequences. Eukaryotic, bacterial, and archaeal linkers are 250, 86, and 73 aa residues in length, respectively, whereas folded domain sequences are 281, 280, and 256 residues, respectively. Cryptic domains match linkers (P < 0.0001) with probabilities ranging between 0.022 and 0.042; accordingly, they do not affect length estimates significantly. Linker sequences support intermolecular binding within proteomes and they are probably enriched in intrinsically disordered regions as well. Reductively evolved linker sequence lengths in growth rate maximized cells should be proportional to proteome diversity. By using total in-frame coding capacity of a genome [i.e., coding sequence (CDS)] as a reliable measure of proteome diversity, we find linker lengths of prokaryotes clearly evolve in proportion to CDS values, whereas those of eukaryotes are more randomly larger than expected. Domain lengths scarcely change over the entire range of CDS values. Thus, the protein linkers of prokaryotes evolve reductively whereas those of eukaryotes do not.
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