Evidence that the root of the tree of life is not within the Archaea

Integrative modeling of gene and genome evolution roots the archaeal tree of life

A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO2 to acetate via the Wood-Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.

The neomuran revolution and phagotrophic origin of eukaryotes and cilia in the light of intracellular coevolution and a revised tree of life

Three kinds of cells exist with increasingly complex membrane-protein targeting: Unibacteria (Archaebacteria, Posibacteria) with one cytoplasmic membrane (CM); Negibacteria with a two-membrane envelope (inner CM; outer membrane [OM]); eukaryotes with a plasma membrane and topologically distinct endomembranes and peroxisomes. I combine evidence from multigene trees, palaeontology, and cell biology to show that eukaryotes and archaebacteria are sisters, forming the clade neomura that evolved ~1.2 Gy ago from a posibacterium, whose DNA segregation and cell division were destabilized by murein wall loss and rescued by the evolving novel neomuran endoskeleton, histones, cytokinesis, and glycoproteins. Phagotrophy then induced coevolving serial major changes making eukaryote cells, culminating in two dissimilar cilia via a novel gliding-fishing-swimming scenario. I transfer Chloroflexi to Posibacteria, root the universal tree between them and Heliobacteria, and argue that Negibacteria are a clade whose OM, evolving in a green posibacterium, was never lost.

The deep roots of the rings of life

Reconstructing early evolutionary events like the origins of informational and operational genes, membranes, and photophosphorylation is difficult because early evolutionary events can be masked by subsequent gene flows. Furthermore, as evolution progresses through both Darwinian survival of the fittest (tree-like evolution) and symbiotic/endosymbiotic cooperation (ring-like evolution), trees alone are not adequate to represent Earth's evolutionary history. Here, we reconstruct and root the New Rings of Life and use it as a framework for interpreting early events in the evolution of life. Unlike the three-domain hypothesis, the rings do not fit all life into one of three immutable categories, but rather accommodate new gene flows as novel organisms are discovered. A draft of the Rooted Rings of Life is reconstructed by analyzing the phylogenetic distributions of indels (insertions/deletions) and genes coding for fundamental molecular processes. Their phylogenetic distributions are inconsistent with all trees. Hypergeometric distribution analyses of them strongly localize the root of the rings to a segment of the deepest ring (P < 10(-21) and P < 10(-194)), and whole-genome analyses independently confirm the topology of the rooted rings (P < 7.1 × 10(-6)). The rings identify several large gene flows, including a flow of a thousand genes into the Halobacteria and the Eubacteria, the related photocyte flow, the flow of genes into the last common ancestor of the eocytes and the eukaryotes, and the informational and operational gene flows into the eukaryotes. The rooted rings also chronologically order steps in the evolution of extant taxa, that is, phototrophy evolved from Halobacteria (photophosphorylation) → Heliobacteria (photosynthesis) → Cyanobacteria (oxygenic photosynthesis).

The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon

BACKGROUND

The tree of life is usually rooted between archaea and bacteria. We have previously presented three arguments that support placing the root of the tree of life in bacteria. The data have been dismissed because those who support the canonical rooting between the prokaryotic superkingdoms cannot imagine how the vast divide between the prokaryotic superkingdoms could be crossed.

RESULTS

We review the evidence that archaea are derived, as well as their biggest differences with bacteria. We argue that using novel data the gap between the superkingdoms is not insurmountable. We consider whether archaea are holophyletic or paraphyletic; essential to understanding their origin. Finally, we review several hypotheses on the origins of archaea and, where possible, evaluate each hypothesis using bioinformatics tools. As a result we argue for a firmicute ancestry for archaea over proposals for an actinobacterial ancestry.

CONCLUSION

We believe a synthesis of the hypotheses of Lake, Gupta, and Cavalier-Smith is possible where a combination of antibiotic warfare and viral endosymbiosis in the bacilli led to dramatic changes in a bacterium that resulted in the birth of archaea and eukaryotes.

REVIEWERS

This article was reviewed by Patrick Forterre, Eugene Koonin, and Gáspár Jékely.

Biochemical constraints in a protobiotic earth devoid of basic amino acids: the "BAA(-) world"

It has been hypothesized in this journal and elsewhere, based on surveys of published data from prebiotic synthesis experiments and carbonaceous meteorite analyses, that basic amino acids such as lysine and arginine were not abundant on prebiotic Earth. If the basic amino acids were incorporated only rarely into the first peptides formed in that environment, it is important to understand what protobiotic chemistry is possible in their absence. As an initial test of the hypothesis that basic amino acid negative [BAA(-)] proteins could have performed at least a subset of protobiotic chemistry, the current work reports on a survey of 13 archaeal and 13 bacterial genomes that has identified 61 modern gene sequences coding for known or putative proteins not containing arginine or lysine. Eleven of the sequences found code for proteins whose functions are well known and important in the biochemistry of modern microbial life: lysine biosynthesis protein LysW, arginine cluster proteins, copper ion binding proteins, bacterial flagellar proteins, and PE or PPE family proteins. These data indicate that the lack of basic amino acids does not prevent peptides or proteins from serving useful structural and biochemical functions. However, as would be predicted from fundamental physicochemical principles, we see no fossil evidence of prebiotic BAA(-) peptide sequences capable of interacting directly with nucleic acids.

Genome networks root the tree of life between prokaryotic domains

Eukaryotes arose from prokaryotes, hence the root in the tree of life resides among the prokaryotic domains. The position of the root is still debated, although pinpointing it would aid our understanding of the early evolution of life. Because prokaryote evolution was long viewed as a tree-like process of lineage bifurcations, efforts to identify the most ancient microbial lineage split have traditionally focused on positioning a root on a phylogenetic tree constructed from one or several genes. Such studies have delivered widely conflicting results on the position of the root, this being mainly due to methodological problems inherent to deep gene phylogeny and the workings of lateral gene transfer among prokaryotes over evolutionary time. Here, we report the position of the root determined with whole genome data using network-based procedures that take into account both gene presence or absence and the level of sequence similarity among all individual gene families that are shared across genomes. On the basis of 562,321 protein-coding gene families distributed across 191 genomes, we find that the deepest divide in the prokaryotic world is interdomain, that is, separating the archaebacteria from the eubacteria. This result resonates with some older views but conflicts with the results of most studies over the last decade that have addressed the issue. In particular, several studies have suggested that the molecular distinctness of archaebacteria is not evidence for their antiquity relative to eubacteria but instead stems from some kind of inherently elevated rate of archaebacterial sequence change. Here, we specifically test for such a rate elevation across all prokaryotic lineages through the analysis of all possible quartets among eight genes duplicated in all prokaryotes, hence the last common ancestor thereof. The results show that neither the archaebacteria as a group nor the eubacteria as a group harbor evidence for elevated evolutionary rates in the sampled genes, either in the recent evolutionary past or in their common ancestor. The interdomain prokaryotic position of the root is thus not attributable to lineage-specific rate variation.

Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution

BACKGROUND

The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long-standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis.

RESULTS

I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation advantages. These successive changes took place in naked growing cells, probably as indirect consequences of the origin of phagotrophy. The first eukaryote had 1-2 cilia and also walled resting cysts; I outline how encystation may have promoted the origin of meiotic sex. I also explain why many alternative ideas are inadequate.

CONCLUSION

Nuclear pore complexes are evolutionary chimaeras of endomembrane- and mitosis-related chromatin-associated proteins. The keys to understanding eukaryogenesis are a proper phylogenetic context and understanding organelle coevolution: how innovations in one cell component caused repercussions on others.

Genome beginnings: rooting the tree of life

A rooted tree of life provides a framework to answer central questions about the evolution of life. Here we review progress on rooting the tree of life and introduce a new root of life obtained through the analysis of indels, insertions and deletions, found within paralogous gene sets. Through the analysis of indels in eight paralogous gene sets, the root is localized to the branch between the clade consisting of the Actinobacteria and the double-membrane (Gram-negative) prokaryotes and one consisting of the archaebacteria and the firmicutes. This root provides a new perspective on the habitats of early life, including the evolution of methanogenesis, membranes and hyperthermophily, and the speciation of major prokaryotic taxa. Our analyses exclude methanogenesis as a primitive metabolism, in contrast to previous findings. They parsimoniously imply that the ether archaebacterial lipids are not primitive and that the cenancestral prokaryotic population consisted of organisms enclosed by a single, ester-linked lipid membrane, covered by a peptidoglycan layer. These results explain the similarities previously noted by others between the lipid synthesis pathways in eubacteria and archaebacteria. The new root also implies that the last common ancestor was not hyperthermophilic, although moderate thermophily cannot be excluded.

Evidence for an early prokaryotic endosymbiosis

Endosymbioses have dramatically altered eukaryotic life, but are thought to have negligibly affected prokaryotic evolution. Here, by analysing the flows of protein families, I present evidence that the double-membrane, gram-negative prokaryotes were formed as the result of a symbiosis between an ancient actinobacterium and an ancient clostridium. The resulting taxon has been extraordinarily successful, and has profoundly altered the evolution of life by providing endosymbionts necessary for the emergence of eukaryotes and by generating Earth's oxygen atmosphere. Their double-membrane architecture and the observed genome flows into them suggest a common evolutionary mechanism for their origin: an endosymbiosis between a clostridium and actinobacterium.

Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life

Background

The root of the tree of life has been a holy grail ever since Darwin first used the tree as a metaphor for evolution. New methods seek to narrow down the location of the root by excluding it from branches of the tree of life. This is done by finding traits that must be derived, and excluding the root from the taxa those traits cover. However the two most comprehensive attempts at this strategy, performed by Cavalier-Smith and Lake et al., have excluded each other's rootings.

Results

The indel polarizations of Lake et al. rely on high quality alignments between paralogs that diverged before the last universal common ancestor (LUCA). Therefore, sequence alignment artifacts may skew their conclusions. We have reviewed their data using protein structure information where available. Several of the conclusions are quite different when viewed in the light of structure which is conserved over longer evolutionary time scales than sequence. We argue there is no polarization that excludes the root from all Gram-negatives, and that polarizations robustly exclude the root from the Archaea.

Conclusion

We conclude that there is no contradiction between the polarization datasets. The combination of these datasets excludes the root from every possible position except near the Chloroflexi.

Reviewers

This article was reviewed by Greg Fournier (nominated by J. Peter Gogarten), Purificación López-García, and Eugene Koonin.

Evolutionary persistence of the molybdopyranopterin-containing sulfite oxidase protein fold

SUMMARY

The importance of molybdoenzymes is exemplified both by the debilitating and fatal human diseases caused by their deficiency and by their persistence throughout evolution. Here, we show that the protein fold of the molybdopyranopterin-containing domain of sulfite oxidase (the SUOX fold) can be found in all three domains of life. Analyses of sequence data and protein structure comparisons (secondary structure matching) show that the SUOX fold is found in enzymes that have quite distinct macromolecular architectures comprising one or more domains and sometimes subsidiary subunits. These are summarized as follows: (i) animal SUOXs that contain an N-terminal cytochrome b(5) domain and an SUOX fold fused to a C-terminal dimerization domain; (ii) plant SUOX that contains an SUOX fold fused to a C-terminal dimerization domain; (iii) the YedY protein from Escherichia coli, which comprises only the SUOX fold; (iv) the sulfite dehydrogenase from Starkeya novella that contains the SUOX fold, a dimerization domain, and an additional c-type cytochrome subunit; and (v) the plant-type nitrate reductases, exemplified by that of Pichia angusta, that contain an N-terminal SUOX fold, a dimerization domain, a cytochrome b(5) domain, and a C-terminal NADH binding flavin adenine dinucleotide-containing domain. We used the primary sequences of the proteins containing an SUOX fold to mine 559 sequences of related proteins. A phylogeny of a nonredundant subset of these sequences was generated, and the resultant clades were categorized by sequence motif analyses in the context of the available protein structures. Based on the motif analyses, cladistics, and domain conservations, we are able to postulate a plausible pathway of SUOX fold enzyme evolution.

Transfer RNA and the origins of diversified life

The evolution of the transfer RNA (tRNA) molecule is controversial but embeds the history of protein biosynthesis, the genetic code, and the origins of diversified life. A new phylogenetic method based on RNA structure that we developed provides new lines of evidence to support the genome tag hypothesis and confirms that the 'top half' of tRNA is more ancient than the 'bottom half'. Timelines of amino acid charging function generated from constraint analyses showed that selenocysteine, tyrosine, serine, and leucine specificities were ancient, while those related to asparagine, methionine, and arginine were more recent. The timelines also uncovered an early role of the second and then first codon bases, identified codons for alanine and proline as the most ancient, and revealed important evolutionary take-overs related to the loss of the long variable arm of tRNA. Furthermore, organismal timelines showed Archaea was the oldest superkingdom, followed by viruses, and superkingdoms Eukarya and Bacteria in that order supporting conclusions from recent phylogenomic studies of protein architecture. Strikingly, results showed that the origin of viruses was not only ancient but was linked to Archaea, supporting the notion that the archaeal lineage is the most ancient on earth and its origin predated diversification of tRNA function and specificity.

Can identification of a fourth domain of life be made from sequence data alone, and could it be done on Mars?

A central question in astrobiology is whether life exists elsewhere in the universe. If so, is it related to Earth life? Technologies exist that enable identification of DNA- or RNA-based microbial life directly from environmental samples here on Earth. Such technologies could, in principle, be applied to the search for life elsewhere; indeed, efforts are underway to initiate such a search. However, surveying for nucleic acid-based life on other planets, if attempted, must be carried out with caution, owing to the risk of contamination by Earth-based life. Here we argue that the null hypothesis must be that any DNA discovered and sequenced from samples taken elsewhere in the universe are Earth-based contaminants. Experience from studies of low-biomass ancient DNA demonstrates that some results, by their very nature, will not enable complete rejection of the null hypothesis. In terms of eliminating contamination as an explanation of the data, there may be value in identification of sequences that lie outside the known diversity of the three domains of life. We therefore have examined whether a fourth domain could be readily identified from environmental DNA sequence data alone. We concluded that, even on Earth, this would be far from trivial, and we illustrate this point by way of examples drawn from the literature. Overall, our conclusions do not bode well for planned PCR-based surveys for life on Mars, and we argue that other independent biosignatures will be essential in corroborating any claims for the presence of life based on nucleic acid sequences.

Protein disulfide oxidoreductases and the evolution of thermophily: was the last common ancestor a heat-loving microbe?

Protein disulfide oxidoreductases (PDOs) are redox enzymes that catalyze dithiol-disulfide exchange reactions. Their sequences and structure reveal the presence of two thioredoxin fold units, each of which is endowed with a catalytic site CXXC motif. PDOs are the outcome of an ancient gene duplication event. They have been described in a number of thermophilic and hyperthermophilic species, where they play a critical role in the structural stabilization of intracellular proteins. PDOs are homologous to both the N-terminal domain of the bacterial alkyl hydroperoxide reductase (AhpF) and to the eukaryotic protein disulfide isomerase (PDI). Phylogenetic analysis of PDOs suggests that they first evolved in the crenarchaeota, spreading from them into the Bacteria via the euryarchaeota. These results imply that the last common ancestor (LCA) of all extant living beings lacked a PDO and argue, albeit weakly, against a thermophilic LCA.

Polyphasic evidence delineating the root of life and roots of biological domains

Twenty different lines of polyphasic evidence obtained from tRNA and protein sequences, anticodon usages, gene contents, metabolism and geochemistry have made possible the identification of a Last Universal Common Ancestor (LUCA) phylogenetically located proximal to the hyperthermophilic methanogenic archaeon Methanopyrus. Combined with analysis of high-similarity cross-domain tRNA pairs, the evidence also suggests a Thermotoga-proximal Last Bacterial Common Ancestor (LBACA) that originated from Crenarchaeota close to Aeropyrum, and a Plasmodium-proximal Last Eukaryotic Common Ancestor (LECA) derived from Ferroplasma through endosymbiosis.

The evidence that the tree life is not rooted within the Archaea is unreliable: A reply to Skophammer et al

Skophammer et al. [Skophammer, RG, Herbold, CW, Rivera, MC, Servin, JA, Lake, JA. 2006. Evidence that the root of the tree of life is not within the Archaea. Mol Biol Evol, 23, 1648-1651] report evidence suggesting that the tree of life cannot be rooted within the Archaea domain. I have observed that an alignment used in their analysis is not reliable and that, therefore, their conclusions are unjustified.

Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis

BACKGROUND

The Archaea are highly diverse in terms of their physiology, metabolism and ecology. Presently, very few molecular characteristics are known that are uniquely shared by either all archaea or the different main groups within archaea. The evolutionary relationships among different groups within the Euryarchaeota branch are also not clearly understood.

RESULTS

We have carried out comprehensive analyses on each open reading frame (ORFs) in the genomes of 11 archaea (3 Crenarchaeota--Aeropyrum pernix, Pyrobaculum aerophilum and Sulfolobus acidocaldarius; 8 Euryarchaeota--Pyrococcus abyssi, Methanococcus maripaludis, Methanopyrus kandleri, Methanococcoides burtonii, Halobacterium sp. NCR-1, Haloquadratum walsbyi, Thermoplasma acidophilum and Picrophilus torridus) to search for proteins that are unique to either all Archaea or for its main subgroups. These studies have identified 1448 proteins or ORFs that are distinctive characteristics of Archaea and its various subgroups and whose homologues are not found in other organisms. Six of these proteins are unique to all Archaea, 10 others are only missing in Nanoarchaeum equitans and a large number of other proteins are specific for various main groups within the Archaea (e.g. Crenarchaeota, Euryarchaeota, Sulfolobales and Desulfurococcales, Halobacteriales, Thermococci, Thermoplasmata, all methanogenic archaea or particular groups of methanogens). Of particular importance is the observation that 31 proteins are uniquely present in virtually all methanogens (including M. kandleri) and 10 additional proteins are only found in different methanogens as well as A. fulgidus. In contrast, no protein was exclusively shared by various methanogen and any of the Halobacteriales or Thermoplasmatales. These results strongly indicate that all methanogenic archaea form a monophyletic group exclusive of other archaea and that this lineage likely evolved from Archaeoglobus. In addition, 15 proteins that are uniquely shared by M. kandleri and Methanobacteriales suggest a close evolutionary relationship between them. In contrast to the phylogenomics studies, a monophyletic grouping of archaea is not supported by phylogenetic analyses based on protein sequences.

CONCLUSION

The identified archaea-specific proteins provide novel molecular markers or signature proteins that are distinctive characteristics of Archaea and all of its major subgroups. The species distributions of these proteins provide novel insights into the evolutionary relationships among different groups within Archaea, particularly regarding the origin of methanogenesis. Most of these proteins are of unknown function and further studies should lead to discovery of novel biochemical and physiological characteristics that are unique to either all archaea or its different subgroups.

Rooting the tree of life using nonubiquitous genes

Insertion and deletion (indel)-based analyses have great potential for rooting the tree of life, but their use has been limited because they require ubiquitous sequences that have not been horizontally/laterally transferred. Very few such sequences exist. Here we describe and demonstrate a new algorithm that can use nonubiquitous sequences for rooting. This algorithm, top-down indel rooting, uses the traditional logical framework of indel rooting, but by considering gene gains and losses in addition to indel gains and losses, it is able to analyze incomplete data sets. The method is demonstrated using theoretical examples and incomplete gene sets. In particular, it is applied to the well-studied Hsp70/MreB indel, a sequence set thought to have been compromised by gene transfers from Firmicutes to archaebacteria. By sequentially assigning all observable character states, including gene absences, to the questionable archaebacterial Hsp70 and MreB sequences, we demonstrate that this gene set robustly excludes the root of the tree of life from the Gram-negative, double-membrane prokaryotes independently of the archaeal character states. There are very few ubiquitous paralog gene sets, and most of them contain compromised data. The ability of top-down rooting to use incomplete and/or compromised gene sets promises to make rooting analyses more robust and to greatly increase the number of useful indel sets.