The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner

Glansdorff, Nicolas; Xu, Ying; Labedan, Bernard

doi:10.1186/1745-6150-3-29

Cited by 223 publications

(150 citation statements)

References 209 publications

(326 reference statements)

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“…Under such a scenario (the so-called proto-eukaryote hypothesis; e.g., ref. 67), a lineage of amitochondriate, nucleated proto-eukaryotes would have existed, before the acquisition of the mitochondrion. Multiple lines of evidence, however, have been used to criticize this particular fusion model.…”

Section: Resultsmentioning

confidence: 99%

Gene similarity networks provide tools for understanding eukaryote origins and evolution

Alvarez‐Ponce

Lopez

Bapteste

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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The complexity and depth of the relationships between the three domains of life challenge the reliability of phylogenetic methods, encouraging the use of alternative analytical tools. We reconstructed a gene similarity network comprising the proteomes of 14 eukaryotes, 104 prokaryotes, 2,389 viruses and 1,044 plasmids. This network contains multiple signatures of the chimerical origin of Eukaryotes as a fusion of an archaebacterium and a eubacterium that could not have been observed using phylogenetic trees. A number of connected components (gene sets with stronger similarities than expected by chance) contain pairs of eukaryotic sequences exhibiting no direct detectable similarity. Instead, many eukaryotic sequences were indirectly connected through a "eukaryote-archaebacterium-eubacterium-eukaryote" similarity path. Furthermore, eukaryotic genes highly connected to prokaryotic genes from one domain tend not to be connected to genes from the other prokaryotic domain. Genes of archaebacterial and eubacterial ancestry tend to perform different functions and to act at different subcellular compartments, but in such an intertwined way that suggests an early rather than late integration of both gene repertoires. The archaebacterial repertoire has a similar size in all eukaryotic genomes whereas the number of eubacteriumderived genes is much more variable, suggesting a higher plasticity of this gene repertoire. Consequently, highly reduced eukaryotic genomes contain more genes of archaebacterial than eubacterial affinity. Connected components with prokaryotic and eukaryotic genes tend to include viral and plasmid genes, compatible with a role of gene mobility in the origin of Eukaryotes. Our analyses highlight the power of network approaches to study deep evolutionary events.mobile genetic elements | cellular evolution | network analysis | organelles | recombination

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Section: Resultsmentioning

confidence: 99%

Gene similarity networks provide tools for understanding eukaryote origins and evolution

Alvarez‐Ponce

Lopez

Bapteste

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…Mesophile (Glansdorff et al 2008) LUCA Archaea have a uniform membrane lipid composition that is suited to life at extreme conditions (heat and pH); in contrast, bacterial membranes show a high variability in composition. The authors suggest that Archaea emerged from a nonthermophilic LUCA under strong selective pressure for adaptation to high temperature; whereas, bacteria were initially nonthermophilic and adapted by convergent evolution to high temperatures.…”

Section: Ancestral Sequence Reconstructionmentioning

confidence: 99%

Deep Phylogeny--How a Tree Can Help Characterize Early Life on Earth

Gaucher

Kratzer²,

Randall³

2009

Cold Spring Harbor Perspectives in Biology

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“…Most researchers agree on the existence of an "RNA-Protein World" stage preceeding the divergence of Eubacteria, Archaea, and Eukarya, in which genetic information was stored in RNA [24,61,140,168,187]. Two competing theories postulate either a last common ancestor (LUCA) of the three domains with a DNA genome [13,109], or a LUCA with an RNA genome [41,55,61,89,133]. In the latter scenario, the transition to a DNA genomes occurred twice (once in Eubacteria and once in Archaea+Eukarya) [54] or even thrice [55], possibly mediated by viral entities.…”

Section: Origins Of Dna Genomesmentioning

confidence: 99%

Innovation in gene regulation: The case of chromatin computation

Prohaska

Stadler

Krakauer

2010

Journal of Theoretical Biology

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Chromatin regulation is understood to be one of the fundamental modes of gene regulation in eukaryotic cells. We argue that the basic proteins that determine the chromatin architecture constitute an evolutionary ancient layer of transcriptional regulation common to all three domains of life. We explore phylogenetically, sources of innovation in chromatin regulation, focusing on protein domains related to chromatin structure and function, demonstrating a step-wise increase of complexity in chromatin regulation. Building upon the highly conserved use of variants of chromosomal architectural proteins to distinguish chromosomal states, Eukarya secondarily acquired mechanisms for "writing" chemical modifications onto chromatin that constitute persistent signals. The acquisition of reader domains enabled decoding of these complex, signal combinations and a decoupling of the signal from immediate biochemical effects. We show how the coupling of reading and writing, which is most prevalent in crown-group Eukarya, could have converted chromatin into a powerful computational device capable of storing and processing more information than pure cis-regulatory networks.Key words: Chromatin, gene regulation, evolution Summary of Findings and Evolutionary HypothesisGene regulation in extant organisms is a complex adaptive system making use of a diversity of mechanisms to ensure that proteins and complementary macromolecular components are produced and maintained at functional levels in variable environments.In this contribution we focus on one key regulatory subsystem of the cell: chromatin regulation. We argue that chromatin functioned as general regulator of transcription in the primordial nucleus, and that a series of key molecular innovations has significantly expanded the regulatory scope of the cell. In this section we summarize the key empirical results of the paper. Sections 2 through 6 provide the empirical support for these claims. In section 7, we formulate an evolutionary Email addresses: sonja@bioinf.uni-leipzig.de (Sonja J. Prohaska), studla@bioinf.uni-leipzig.de (Peter F. Stadler), krakauer@santafe.edu (David C. Krakauer) hypothesis that seeks to explain our findings in terms of the evolution of proto-genetic regulation. We then interpret this evolutionary sequence in terms of increasing computational power by locating key stages of the evolutionary sequence within a formal model of computation. Since sections 2-6 are primarily concerned with presenting evidence, those interested in the conceptual development of the argument can focus on sections 7 and 8.Two variants of Chromosomal Architectural Proteins (ChAPs) are sufficient to define binary genomic, and potentially phenotypic, states. We show how extensions to this binary system lead to potential distinctions among an increasing number of genomic states, culminating in forms of control localized to specific sites in the genome, as illustrated for example by extant mammalian histone variants capable of differential expression and/or localization to r...

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The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner

Cited by 223 publications

References 209 publications

Gene similarity networks provide tools for understanding eukaryote origins and evolution

Gene similarity networks provide tools for understanding eukaryote origins and evolution

Deep Phylogeny--How a Tree Can Help Characterize Early Life on Earth

Innovation in gene regulation: The case of chromatin computation

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