scholarly journals An archaeal origin of eukaryotes supports only two primary domains of life

Nature ◽  
2013 ◽  
Vol 504 (7479) ◽  
pp. 231-236 ◽  
Author(s):  
Tom A. Williams ◽  
Peter G. Foster ◽  
Cymon J. Cox ◽  
T. Martin Embley
Keyword(s):  
Domains Of Life ◽  
Origin Of Eukaryotes

scholarly journals A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Monique Aouad ◽  
Jean-Pierre Flandrois ◽  
Frédéric Jauffrit ◽  
Manolo Gouy ◽  
Simonetta Gribaldo ◽  
...  
Keyword(s):  
Phylogenetic Signal ◽  
Single Gene ◽  
Tree Of Life ◽  
Divide And Conquer ◽  
Data Sets ◽  
Gene Trees ◽  
Tree Reconstruction ◽  
Taxonomic Rank ◽  
Domains Of Life ◽  
Origin Of Eukaryotes

Abstract Background The recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life. This has been particularly spectacular concerning the Archaea, projecting them at the center stage as prominently relevant to understand early stages in evolution and the emergence of fundamental metabolisms as well as the origin of eukaryotes. Yet, resolving deep divergences remains a challenging task due to well-known tree-reconstruction artefacts and biases in extracting robust ancient phylogenetic signal, notably when analyzing data sets including the three Domains of Life. Among the various strategies aimed at mitigating these problems, divide-and-conquer approaches remain poorly explored, and have been primarily based on reconciliation among single gene trees which however notoriously lack ancient phylogenetic signal. Results We analyzed sub-sets of full supermatrices covering the whole Tree of Life with specific taxonomic sampling to robustly resolve different parts of the archaeal phylogeny in light of their current diversity. Our results strongly support the existence and early emergence of two main clades, Cluster I and Cluster II, which we name Ouranosarchaea and Gaiarchaea, and we clarify the placement of important novel archaeal lineages within these two clades. However, the monophyly and branching of the fast evolving nanosized DPANN members remains unclear and worth of further study. Conclusions We inferred a well resolved rooted phylogeny of the Archaea that includes all recently described phyla of high taxonomic rank. This phylogeny represents a valuable reference to study the evolutionary events associated to the early steps of the diversification of the archaeal domain. Beyond the specifics of archaeal phylogeny, our results demonstrate the power of divide-and-conquer approaches to resolve deep phylogenetic relationships, which should be applied to progressively resolve the entire Tree of Life.

scholarly journals Why is Life the Way it Is?

2019 ◽  
Vol 03 (01) ◽  
pp. 20-28
Author(s):  
Nick Lane
Keyword(s):  
Common Ancestor ◽  
Structural Constraints ◽  
Last Universal Common Ancestor ◽  
Physical Constraints ◽  
Morphological Complexity ◽  
Metabolic Versatility ◽  
Universal Common Ancestor ◽  
Domains Of Life ◽  
Molecular Machinery ◽  
Origin Of Eukaryotes

The concept of the three domains of life (the bacteria, archaea and eukaryotes) goes back to Carl Woese in 1990 1 . Most scientists now see the eukaryotes (cells with a true nucleus) as a secondary domain, derived from bacteria and archaea via an endosymbiosis 2 . That makes the last universal common ancestor of life (LUCA) the ancestor of bacteria and archaea 3 . While these domains are strikingly different in their genetics and biochemistry 4 , they are nearly indistinguishable in their cellular morphology — historically, both groups have been classed as prokaryotes. In terms of their metabolic versatility and molecular machinery, prokaryotes are if anything more sophisticated than eukaryotes 5 . Yet despite an exhaustive search of genetic sequence space in virtually infinite populations over four billion years, neither domain evolved morphological complexity to compare with eukaryotes 5 . The evolutionary path to morphological complexity does not seem to depend on genetic information alone 6 . The most plausible explanation is that physical constraints stemming from the topological structure of prokaryotes blocked the evolution of morphological complexity in prokaryotes, and that the endosymbiosis at the origin of eukaryotes relieved these constraints 6 . In this lecture, I shall argue that the dependence of all life on electrical charges across membranes to generate energy explains the structural constraints on prokaryotes, and the escape from these constraints in eukaryotes 7 .

scholarly journals The Fennoscandian Shield deep terrestrial virosphere suggests slow motion ‘boom and burst’ cycles

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Karin Holmfeldt ◽  
Emelie Nilsson ◽  
Domenico Simone ◽  
Margarita Lopez-Fernandez ◽  
Xiaofen Wu ◽  
...  
Keyword(s):  
Antibiotic Production ◽  
Nutrient Recycling ◽  
Slow Motion ◽  
Deep Biosphere ◽  
Wide Range ◽  
Domains Of Life ◽  
Microbial Turnover ◽  
Rna Transcript ◽  
Viral Isolates ◽  
Antagonistic Interactions

AbstractThe deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in ‘metabolic standby’. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of ‘kill-the-winner’ oscillations creating slow motion ‘boom and burst’ cycles.

scholarly journals Lipoproteins Are Responsible for the Pro-Inflammatory Property of Staphylococcus aureus Extracellular Vesicles

2021 ◽  
Vol 22 (13) ◽  
pp. 7099
Author(s):  
Pradeep Kumar Kopparapu ◽  
Meghshree Deshmukh ◽  
Zhicheng Hu ◽  
Majd Mohammad ◽  
Marco Maugeri ◽  
...  
Keyword(s):  
Extracellular Vesicles ◽  
Inflammatory Responses ◽  
Surface Proteins ◽  
Host Cells ◽  
Immune Stimulation ◽  
Domains Of Life ◽  
Major Surface ◽  
Staphylococcal Aureus

Staphylococcal aureus (S. aureus), a Gram-positive bacteria, is known to cause various infections. Extracellular vesicles (EVs) are a heterogeneous array of membranous structures secreted by cells from all three domains of life, i.e., eukaryotes, bacteria, and archaea. Bacterial EVs are implied to be involved in both bacteria–bacteria and bacteria–host interactions during infections. It is still unclear how S. aureus EVs interact with host cells and induce inflammatory responses. In this study, EVs were isolated from S. aureus and mutant strains deficient in either prelipoprotein lipidation (Δlgt) or major surface proteins (ΔsrtAB). Their immunostimulatory capacities were assessed both in vitro and in vivo. We found that S. aureus EVs induced pro-inflammatory responses both in vitro and in vivo. However, this activity was dependent on lipidated lipoproteins (Lpp), since EVs isolated from the Δlgt showed no stimulation. On the other hand, EVs isolated from the ΔsrtAB mutant showed full immune stimulation, indicating the cell wall anchoring of surface proteins did not play a role in immune stimulation. The immune stimulation of S. aureus EVs was mediated mainly by monocytes/macrophages and was TLR2 dependent. In this study, we demonstrated that not only free Lpp but also EV-imbedded Lpp had high pro-inflammatory activity.

scholarly journals A Global Review on Short Peptides: Frontiers and Perspectives

Molecules ◽  
2021 ◽  
Vol 26 (2) ◽  
pp. 430
Author(s):  
Vasso Apostolopoulos ◽  
Joanna Bojarska ◽  
Tsun-Thai Chai ◽  
Sherif Elnagdy ◽  
Krzysztof Kaczmarek ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Targeted Delivery ◽  
Swot Analysis ◽  
Functional Materials ◽  
Great Promise ◽  
Short Peptides ◽  
Altered Peptide Ligands ◽  
Short Peptide ◽  
Domains Of Life

Peptides are fragments of proteins that carry out biological functions. They act as signaling entities via all domains of life and interfere with protein-protein interactions, which are indispensable in bio-processes. Short peptides include fundamental molecular information for a prelude to the symphony of life. They have aroused considerable interest due to their unique features and great promise in innovative bio-therapies. This work focusing on the current state-of-the-art short peptide-based therapeutical developments is the first global review written by researchers from all continents, as a celebration of 100 years of peptide therapeutics since the commencement of insulin therapy in the 1920s. Peptide “drugs” initially played only the role of hormone analogs to balance disorders. Nowadays, they achieve numerous biomedical tasks, can cross membranes, or reach intracellular targets. The role of peptides in bio-processes can hardly be mimicked by other chemical substances. The article is divided into independent sections, which are related to either the progress in short peptide-based theranostics or the problems posing challenge to bio-medicine. In particular, the SWOT analysis of short peptides, their relevance in therapies of diverse diseases, improvements in (bio)synthesis platforms, advanced nano-supramolecular technologies, aptamers, altered peptide ligands and in silico methodologies to overcome peptide limitations, modern smart bio-functional materials, vaccines, and drug/gene-targeted delivery systems are discussed.

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