Cross references: The Origin of Life Timeline of Evolution Protobionts
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Searching PubMed for "last common ancestor" found 247 references:
Last Universal Ancestor (Wiki)
"The last universal ancestor (LUA), also called the last universal common ancestor (LUCA), cenancestor, or progenote, is the most recent organism from which all organisms now living on Earth have a common descent. Thus it is the most recent common ancestor (MRCA) of all current life on Earth.
The LUA is estimated to have lived some 3.5 to 3.8 billion years ago (sometime in the Paleoarchean era). The earliest evidence for life on Earth is biogenic graphite found in 3.7 billion-year-old metasedimentary rocks discovered in Western Greenland and microbial mat fossils found in 3.48 billion-year-old sandstone discovered in Western Australia. "
Nature of the Last Universal Ancestor (Goog-PubMed)
"Several scenarios have been proposed during the last years, based on the phylogenies of ribosomal RNA and of duplicated proteins, which suggest that the last universal ancestor was either an RNA progenote or an hyperthermophilic prokaryote."
Horizontal transfer of ATPase genes--the tree of life becomes a net of life.
"An ancient gene duplication gave rise to the catalytic and non-catalytic subunits of each of the three types of proton pumping ATPases: vacuolar, archaebacterial and eubacterial. Previously, this gene duplication has been used to root the universal tree of life. However, recent findings of archaebacterial type ATPases in eubacteria and of eubacterial type in an archaebacterium suggested that both types of ATPases may have been already present in the last common ancestor."
Evolution of glutamate dehydrogenase genes: evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life.
"The existence of two families of genes coding for hexameric glutamate dehydrogenases has been deduced from the alignment of 21 primary sequences and the determination of the percentages of similarity between each pair of proteins. Each family could also be characterized by specific motifs. One family (Family I) was composed of gdh genes from six eubacteria and six lower eukaryotes (the primitive protozoan Giardia lamblia, the green alga Chlorella sorokiniana, and several fungi and yeasts). The other one (Family II) was composed of gdh genes from two eubacteria, two archaebacteria, and five higher eukaryotes (vertebrates)."
I don't understand the importance of glutamate dehydrogenases.
Glutamate dehydrogenase - Wikipedia
Development and diversification of the Last Universal Ancestor.
"The majority of evolutionary steps in the development of basic cellular processes took place in the time interval after the "First Cell" arose until the time of the "Last Universal Ancestor"."
"Interwoven with these developments was the concomitant development of methanogenesis (the third change needed to generate three Kingdoms), which provided the first truly large-scale generation of metabolic energy"
Methanogenesis - Wikipedia
"The terminal electron acceptor in methanogenesis is not oxygen, but carbon. The carbon can occur in a small number of organic compounds, all with low molecular weights. The two best described pathways involve the use of acetic acid and inorganic carbon dioxide as terminal electron acceptors:
Universal protein families and the functional content of the last universal common ancestor.
"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."
Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA virus?
Rewiring the keyboard: evolvability of the genetic code.
"The genetic code evolved in two distinct phases. First, the 'canonical' code emerged before the last universal ancestor; subsequently, this code diverged in numerous nuclear and organelle lineages. Here, we examine the distribution and causes of these secondary deviations from the canonical genetic code. The majority of non-standard codes arise from alterations in the tRNA, with most occurring by post-transcriptional modifications, such as base modification or RNA editing, rather than by substitutions within tRNA anticodons."
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokariots. Free PMC Article
"Comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (HGT), at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution."
"Therefore, the results seem to be compatible with approximately equal likelihoods of HGT and gene loss in the evolution of prokaryotes."
2003 201<247 Free PMC Article
The redox protein construction kit: pre-last universal common ancestor evolution of energy-conserving enzymes.
"Genome analyses and the resolution of three-dimensional structures have provided evidence in recent years for hitherto unexpected family relationships between redox proteins of very diverse enzymes involved in bioenergetic electron transport. Many of these enzymes appear in fact to be constructed from only a limited set of building blocks."
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The universal ancestor was a thermophile or a hyperthermophile: tests and further evidence.
"(1) There is no evidence that the LUCA might have been a mesophile and observations seem to imply that the LUCA was a thermophile or a hyperthermophile;
(2) The ancestors of the Archaea and Bacteria domains seem to be (hyper)thermophiles while that of the Eukarya domain turns out to be a mesophile."
Transfer RNA paralogs: evidence for genetic code-amino acid biosynthesis coevolution and an archaeal root of life
"Overall, the genetic distances between alloacceptor tRNAs yield estimates of how closely clustered in sequence space are the tRNAs in a genome. Among 34 Bacteria, 18 Archaea and 8 Eukarya, Methanopyrus kandleri and Aeropyrum pernix have yielded the lowest alloacceptor distances and largest number of paralogous pairs. Based on a cluster-dispersion model of tRNA evolution, such tight alloacceptor clustering is a measure of primitiveness of tRNA genotypes, and places last universal common ancestor (LUCA) between the branches leading to these two archaea in the tRNA phylogenetic tree."
Modern mRNA proofreading and repair: clues that the last universal common ancestor possessed an RNA genome?
" We have examined the available literature on multisubunit RNA polymerase structure and function and conclude that a strong case can be made that the Last Universal Common Ancestor (LUCA) possessed a repair-competent RNA polymerase, which would have been capable of acting on an RNA genome."
2005 180<247 Free PMC Article
Protein content of minimal and ancestral ribosome.
"A consensus of computational and experimental approaches indicates that a minimal genome is close to 300 protein-coding genes, if a rich medium is provided for cell growth."
The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells.
"Most evolutionists agree to consider that our present RNA/DNA/protein world has originated from a simpler world in which RNA played both the role of catalyst and genetic material."
"The hypothesis that DNA and associated mechanisms (replication, repair, recombination) first evolved and diversified in a world of DNA viruses infecting RNA cells readily explains the existence of viral-encoded DNA transaction proteins without cellular homologues."
On the origin of genomes and cells within inorganic compartments.
"Building on the model of Russell and Hall for the emergence of life at a warm submarine hydrothermal vent, we suggest that, within a hydrothermally formed system of contiguous iron-sulfide (FeS) compartments, populations of virus-like RNA molecules, which eventually encoded one or a few proteins each, became the agents of both variation and selection. The initial darwinian selection was for molecular self-replication. Combinatorial sorting of genetic elements among compartments would have resulted in preferred proliferation and selection of increasingly complex molecular ensembles--those compartment contents that achieved replication advantages.
The last universal common ancestor (LUCA) we propose was not free-living but an inorganically housed assemblage of expressed and replicable genetic elements. The evolution of the enzymatic systems for (i) DNA replication; and (ii) membrane and cell wall biosynthesis, enabled independent escape of the first archaebacterial and eubacterial cells from their hydrothermal hatchery, within which the LUCA itself remained confined."
A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective.
" More precisely, when only prokaryotes are considered, the number varies between 1006 and 1189 gene families while when eukaryotes are also included, this number increases to between 1344 and 1529 families depending on the underlying phylogenetic tree.
Therefore, the common belief that the hypothetical genome of LUCA should resemble those of the smallest extant genomes of obligate parasites is not supported by recent advances in computational genomics. Instead, a fairly complex genome similar to those of free-living prokaryotes, with a variety of functional capabilities including metabolic transformation, information processing, membrane/transport proteins and complex regulation, shared between the three domains of life, emerges as the most likely progenitor of life on Earth"
Toward automatic reconstruction of a highly resolved tree of life.
"Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed and preliminary classifications. For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor."
Protein superfamily evolution and the last universal common ancestor (LUCA).
"By exploiting three-dimensional structure comparison, which is more sensitive than conventional sequence-based methods for detecting remote homology, we have identified a set of 140 ancestral protein domains using very restrictive criteria to minimize the potential error introduced by horizontal gene transfer. These domains are highly likely to have been present in the Last Universal Common Ancestor (LUCA) based on their universality in almost all of 114 completed prokaryotic (Bacteria and Archaea) and eukaryotic genomes. Functional analysis of these ancestral domains reveals a genetically complex LUCA with practically all the essential functional systems present in extant organisms, supporting the theory that life achieved its modern cellular status much before the main kingdom separation (Doolittle 2000). In addition, we have calculated different estimations of the genetic and functional versatility of all the superfamilies and functional groups in the prokaryote subsample. These estimations reveal that some ancestral superfamilies have been more versatile than others during evolution allowing more genetic and functional variation. Furthermore, the differences in genetic versatility between protein families are more attributable to their functional nature rather than the time that they have been evolving. These differences in tolerance to mutation suggest that some protein families have eroded their phylogenetic signal faster than others, hiding in many cases, their ancestral origin and suggesting that the calculation of 140 ancestral domains is probably an underestimate.
The first lines of divergence in the Bacteria domain were the hyperthermophilic organisms, the Thermotogales and the Aquificales, and not the mesophilic Planctomycetales.
"This strengthens the hypothesis that the last universal common ancestor might have been a hyperthermophilic 'organism' and that, more generally, life might have originated at high temperature."
The universal ancestor and the ancestors of Archaea and Bacteria were anaerobes whereas the ancestor of the Eukarya domain was an aerobe.
"The reconstruction of the ancestral sequences of proteins... has led to the following conclusions: the LUCA was an anaerobic 'organism', as were the ancestors of Archaea and Bacteria, whereas the ancestor of Eukarya was an aerobe."
Combinations of ancestral modules in proteins.
"Twenty-seven protein sequence elements, six to nine amino acids long, were extracted from 15 phylogenetically diverse complete prokaryotic proteomes. The elements are present in all of these proteomes, with at least one copy each (omnipresent elements), and have presumably been conserved since the last universal common ancestor (LUCA). All these omnipresent elements are identified in crystallized protein structures as parts of highly conserved closed loops, 25-30 residues long, thus representing the closed-loop modules discovered in 2000 by Berezovsky et al.
The omnipresent peptides make up seven distinct groups, of which the largest groups, Aleph and Beth, contain 18 and four elements, respectively, which are related but different, while five other groups are represented by only one element each. The LUCA modules appear with one or several copies per protein molecule in a variety of combinations depending on the functional identity of the corresponding protein. The functional involvement of individual LUCA modules is outlined on the basis of known protein annotations.
Analyses of all the related sequences in a large, formatted protein sequence space suggest that many, if not all, of the 27 omnipresent elements have a common sequence origin."
The genomics of LUCA.
"The 424 protein encoding genes in the minimum LUCA genome exceed significantly the 150-340 genes estimated to be present in a minimal proteome compatible with life. Thus LUCA was not a minimal organism but the first modern organism equipped with a DNA genome and the universal genetic code."
Was nitric oxide the first deep electron sink?
"Evolutionary histories of enzymes involved in chemiosmotic energy conversion indicate that a strongly oxidizing substrate was available to the last universal common ancestor before the divergence of Bacteria and Archaea.
According to palaeogeochemical evidence, O(2) was not present beyond trace amounts on the early Earth. Based on recent phylogenetic, enzymatic and geochemical results, we propose that, in the earliest Archaean, nitric oxide (NO) and its derivatives nitrate and nitrite served as strongly oxidizing substrates driving the evolution of a bioenergetic pathway related to modern dissimilatory denitrification.
Aerobic respiration emerged later from within this ancestral pathway via adaptation of the enzyme NO reductase to its new substrate, dioxygen."
Ribonucleotide reduction - horizontal transfer of a required function spans all three domains.
"Ribonucleotide reduction is the only de novo pathway for synthesis of deoxyribonucleotides, the building blocks of DNA. The reaction is catalysed by ribonucleotide reductases (RNRs), an ancient enzyme family comprised of three classes."
The advantages and disadvantages of horizontal gene transfer and the emergence of the first species.
"Horizontal Gene Transfer (HGT) is beneficial to a cell if the acquired gene confers a useful function, but is detrimental if the gene has no function, if it is incompatible with existing genes, or if it is a selfishly replicating mobile element. If the balance of these effects is beneficial on average, we would expect cells to evolve high rates of acceptance of horizontally transferred genes, whereas if it is detrimental, cells should reduce the rate of HGT as far as possible. It has been proposed that the rate of HGT was very high in the early stages of prokaryotic evolution, and hence there were no separate lineages of organisms. Only when the HGT rate began to fall, would lineages begin to emerge with their own distinct sets of genes. Evolution would then become more tree-like. This phenomenon has been called the Darwinian Threshold."
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Did evolution select a nonrandom "alphabet" of amino acids?
"Here, we demonstrate unambiguous support for a refined hypothesis: that an optimal set of amino acids would spread evenly across a broad range of values for each fundamental property. Specifically, we show that the standard set of 20 amino acids represents the possible spectra of size, charge, and hydrophobicity more broadly and more evenly than can be explained by chance alone."
The proteomic complexity and rise of the primordial ancestor of diversified life.
"The last universal common ancestor represents the primordial cellular organism from which diversified life was derived. This urancestor accumulated genetic information before the rise of organismal lineages and is considered to be either a simple 'progenote' organism with a rudimentary translational apparatus or a more complex 'cenancestor' with almost all essential biological processes. Recent comparative genomic studies support the latter model and propose that the urancestor was similar to modern organisms in terms of gene content.
... urancestors were always placed at their base and rooted the tree of life in Archaea.
... confirms diversified life emerged about 2.9 billion years ago during the start of planet oxygenation." Free PMC Article
Comparative analysis of RNA families reveals distinct repertoires for each domain of life.
"However, with limited interdomain transfer and few RNA families exhibiting demonstrable antiquity as predicted under RNA world continuity, our results indicate that the majority of modern cellular RNA repertoires have primarily evolved in a domain-specific manner."
Looking for the Last Universal Common Ancestor (LUCA).
"The thermodynamic tenet clarifies that evolution is a path-dependent process of least-time consumption of free energy. The natural process is without a demarcation line between animate and inanimate."
2012 81<247 Free PMC Article
The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms.
"The evolution of functions that are associated with corresponding Fold Families (FFs) along the timeline reveals that primordial metabolic domains evolved earlier than informational domains involved in translation and transcription, supporting the metabolism-first hypothesis rather than the RNA world scenario. In addition, phylogenomic trees of proteomes reconstructed from FFs appearing in each of the five phases of the protein world show that trees reconstructed from ancient domain structures were consistently rooted in archaeal lineages, supporting the proposal that the archaeal ancestor is more ancient than the ancestors of other superkingdoms."
Towards functional repertoire of the earliest proteins.
"No enzymes involved in metabolic activities are present in the list of the earliest proteins derived by this approach."
Evidence for the existence of elaborate enzyme complexes in the Paleoarchean era.
" Our findings suggest that the evolution of highly efficient enzymes and enzyme complexes has already been completed in the LUCA era, which means that sophisticated catalytic concepts such as substrate channeling and allosteric communication existed already 3.5 billion years ago. "
Prebiotic RNA synthesis by Montmorillonite catalysis.
See: Montmorillonite .
Evolution of the first genetic cells and the universal genetic code: a hypothesis based on macromolecular coevolution of RNA and proteins.
Ancient horizontal gene transfer and the last common ancestors.
"Organisms existing as part of a diverse ecosystem at the time of LUCA likely shared genetic material between lineages."
Free PMC Article
A universal trend among proteomes indicates an oily last common ancestor.
PMID:23300421 Free PMC Article