scholarly journals The Dispersed Archaeal Eukaryome and the Complex Archaeal Ancestor of Eukaryotes

2014 ◽  
Vol 6 (4) ◽  
pp. a016188-a016188 ◽  
Author(s):  
E. V. Koonin ◽  
N. Yutin
Keyword(s):  
Archaeal Ancestor

The comparative biochemistry of viruses and humans: an evolutionary path towards autoimmunity

2019 ◽  
Vol 400 (5) ◽  
pp. 629-638 ◽  
Author(s):  
Darja Kanduc
Keyword(s):  
Measles Virus ◽  
Influenza A ◽  
Viral Infections ◽  
Sequence Similarity ◽  
Eukaryotic Cell ◽  
Point Of View ◽  
Peptide Sequence ◽  
Human Viruses ◽  
Archaeal Ancestor ◽  
Borna Disease

Abstract Analyses of the peptide sharing between five common human viruses (Borna disease virus, influenza A virus, measles virus, mumps virus and rubella virus) and the human proteome highlight a massive viral vs. human peptide overlap that is mathematically unexpected. Evolutionarily, the data underscore a strict relationship between viruses and the origin of eukaryotic cells. Indeed, according to the viral eukaryogenesis hypothesis and in light of the endosymbiotic theory, the first eukaryotic cell (our lineage) originated as a consortium consisting of an archaeal ancestor of the eukaryotic cytoplasm, a bacterial ancestor of the mitochondria and a viral ancestor of the nucleus. From a pathologic point of view, the peptide sequence similarity between viruses and humans may provide a molecular platform for autoimmune crossreactions during immune responses following viral infections/immunizations.

scholarly journals Nucleogenesis and origin of organelles

2008 ◽  
Vol 16 (3-4) ◽  
pp. 88-92
Author(s):  
Milanko Stupar
Keyword(s):  
Replication Fork ◽  
Genome Duplication ◽  
Genetic Recombination ◽  
Mitochondrial Gene ◽  
Strand Break ◽  
Monophyletic Origin ◽  
Double Stranded Dna ◽  
Rigid Cell Wall ◽  
Step Mechanism ◽  
Archaeal Ancestor

Division of the ancestral prokaryotic pragenome into two circular double-stranded DNA molecules by genetic recombination is a base for the future separate evolution of the nuclear and mitochondrial gene compartment. This suggests monophyletic origin of both mitochondrion and nucleus. Presumed organism which genome undergoes genetic recombination has to be searched among an aerobic, oxygen non-producing archaeon with no rigid cell wall, but a plasma membrane. Plastids evolve from an aerobic, oxygen producing proto-eukaryot, after mitoplastide genome duplication and subsequent functional segregation. In this proposal, origin of eukaryots occurs by a three-step mechanism. First, replication fork pauses and collapses generating a breakage in the genome of archaeal ancestor of eukaryots. Second, the double-strand break can be repaired intergenomically by complementary strands invasion. Third, this duplicated genome can be fissioned into two compartments by reciprocal genetic recombination. Scenario is accomplished by aberrant fission of the inner membrane surrounding separately those two compartments.

scholarly journals Calpains in Cyanobacteria and the Origin of Calpains

2021 ◽  
Author(s):  
Dominika Vešelényiová ◽  
Lenka Raabová ◽  
Mária Schneiderová ◽  
Matej Vesteg ◽  
Juraj Krajčovič
Keyword(s):  
Phylogenetic Analysis ◽  
In Silico ◽  
Interaction Analysis ◽  
Cysteine Proteases ◽  
Core Domain ◽  
Cellular Processes ◽  
Cyanobacterial Species ◽  
Interaction Partners ◽  
Archaeal Ancestor ◽  
Calpain Gene

Abstract Calpains are cysteine proteases involved in many cellular processes. They are an ancient and large superfamily of enzymes responsible for the cleavage and irreversible modification of a large variety of substrates. They have been intensively studied in humans and other mammals, but information about calpains in bacteria is scarce. Calpains have not been found among Archaea to date. In this study, we have investigated the presence of calpains in selected cyanobacterial species using in silico analyses. We show that calpains defined by possessing CysPC core domain are present in cyanobacterial genera Anabaena, Aphanizomenon, Calothrix, Chamaesiphon, Fischerella, Microcystis, Scytonema and Trichormus. Based on in silico protein interaction analysis, we have predicted putative interaction partners for identified cyanobacterial calpains. The phylogenetic analysis including cyanobacterial, other bacterial and eukaryotic calpains divided bacterial and eukaryotic calpains into two separate monophyletic clusters. We propose two possible evolutionary scenarios to explain this tree topology: 1) the eukaryotic ancestor or an archaeal ancestor of eukaryotes obtained calpain gene from an unknown bacterial donor, or alternatively 2) calpain gene had been already present in the last common universal ancestor and subsequently lost by the ancestor of Archaea, but retained by the ancestor of Bacteria and by the ancestor of Eukarya. Both scenarios would require multiple independent losses of calpain genes in various bacteria and eukaryotes.

scholarly journals The Common Ancestor of Archaea and Eukarya Was Not an Archaeon

Archaea ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-18 ◽  
Author(s):  
Patrick Forterre
Keyword(s):  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Critical Role ◽  
Last Common Ancestor ◽  
Dna Viruses ◽  
The Common ◽  
Basic Features ◽  
Origin Of Eukaryotes ◽  
Archaeal Ancestor ◽  
Selection Of

It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the “prokaryotic” phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.

scholarly journals Arguments Reinforcing the Three-Domain View of Diversified Cellular Life

Archaea ◽  
2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Arshan Nasir ◽  
Kyung Mo Kim ◽  
Violette Da Cunha ◽  
Gustavo Caetano-Anollés
Keyword(s):  
Cell Movement ◽  
Protein Domain ◽  
Bacterial Cells ◽  
Domain Structures ◽  
Cellular Life ◽  
Protein Domain Structure ◽  
Gain Loss ◽  
Cellular Compartments ◽  
Origin Of Eukaryotes ◽  
Archaeal Ancestor

The archaeal ancestor scenario (AAS) for the origin of eukaryotes implies the emergence of a new kind of organism from the fusion of ancestral archaeal and bacterial cells. Equipped with this “chimeric” molecular arsenal, the resulting cell would gradually accumulate unique genes and develop the complex molecular machineries and cellular compartments that are hallmarks of modern eukaryotes. In this regard, proteins related to phagocytosis and cell movement should be present in the archaeal ancestor, thus identifying the recently described candidate archaeal phylum “Lokiarchaeota” as resembling a possible candidate ancestor of eukaryotes. Despite its appeal, AAS seems incompatible with the genomic, molecular, and biochemical differences that exist between Archaea and Eukarya. In particular, the distribution of conserved protein domain structures in the proteomes of cellular organisms and viruses appears hard to reconcile with the AAS. In addition, concerns related to taxon and character sampling, presupposing bacterial outgroups in phylogenies, and nonuniform effects of protein domain structure rearrangement and gain/loss in concatenated alignments of protein sequences cast further doubt on AAS-supporting phylogenies. Here, we evaluate AAS against the traditional “three-domain” world of cellular organisms and propose that the discovery of Lokiarchaeota could be better reconciled under the latter view, especially in light of several additional biological and technical considerations.

scholarly journals The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of Archaea via a 3′-end cleavage mode

2020 ◽  
Vol 48 (17) ◽  
pp. 9589-9605 ◽  
Author(s):  
Lei Yue ◽  
Jie Li ◽  
Bing Zhang ◽  
Lei Qi ◽  
Zhihua Li ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Termination ◽  
Methanococcus Maripaludis ◽  
Genome Wide ◽  
Transcription Termination Factor ◽  
A Genome ◽  
Archaeal Transcription ◽  
Archaeal Ancestor

Abstract Transcription termination defines accurate transcript 3′-ends and ensures programmed transcriptomes, making it critical to life. However, transcription termination mechanisms remain largely unknown in Archaea. Here, we reported the physiological significance of the newly identified general transcription termination factor of Archaea, the ribonuclease aCPSF1, and elucidated its 3′-end cleavage triggered termination mechanism. The depletion of Mmp-aCPSF1 in Methanococcus maripaludis caused a genome-wide transcription termination defect and disordered transcriptome. Transcript-3′end-sequencing revealed that transcriptions primarily terminate downstream of a uridine-rich motif where Mmp-aCPSF1 performed an endoribonucleolytic cleavage, and the endoribonuclease activity was determined to be essential to the in vivo transcription termination. Co-immunoprecipitation and chromatin-immunoprecipitation detected interactions of Mmp-aCPSF1 with RNA polymerase and chromosome. Phylogenetic analysis revealed that the aCPSF1 orthologs are ubiquitously distributed among the archaeal phyla, and two aCPSF1 orthologs from Lokiarchaeota and Thaumarchaeota could replace Mmp-aCPSF1 to terminate transcription of M. maripaludis. Therefore, the aCPSF1 dependent termination mechanism could be widely employed in Archaea, including Lokiarchaeota belonging to Asgard Archaea, the postulated archaeal ancestor of Eukaryotes. Strikingly, aCPSF1-dependent archaeal transcription termination reported here exposes a similar 3′-cleavage mode as the eukaryotic RNA polymerase II termination, thus would shed lights on understanding the evolutionary linking between archaeal and eukaryotic termination machineries.

scholarly journals Evidence supporting a viral origin of the eukaryotic nucleus

2019 ◽  
Author(s):  
Philip JL Bell
Keyword(s):  
Nuclear Export ◽  
Common Ancestor ◽  
Eukaryotic Cell ◽  
Viral Origin ◽  
Eukaryotic Nucleus ◽  
Complex Process ◽  
Bona Fide ◽  
Viral Factory ◽  
Acting In Concert ◽  
Archaeal Ancestor

AbstractThe defining feature of the eukaryotic cell is the possession of a nucleus that uncouples transcription from translation. This uncoupling of transcription from translation depends on a complex process employing hundreds of eukaryotic specific genes acting in concert and requires the 7-methylguanylate (m7G) cap to prime eukaryotic mRNA for splicing, nuclear export, and cytoplasmic translation. The origin of this complex system is currently a paradox since it is not found or needed in prokaryotic cells which lack nuclei, yet it was apparently present and fully functional in the Last Eukaryotic Common Ancestor (LECA). According to the Viral Eukaryogenesis (VE) hypothesis the abrupt appearance of the nucleus in the eukaryotic lineage occurred because the nucleus descends from the viral factory of a DNA phage that infected the archaeal ancestor of the eukaryotes. Consequently, the system for uncoupling of transcription from translation in eukaryotes is predicted by the VE hypothesis to be viral in origin. In support of this hypothesis it is shown here that m7G capping apparatus that primes the uncoupling of transcription from translation in eukaryotes is present in viruses of the Mimiviridae but absent from bona-fide archaeal relatives of the eukaryotes such as Lokiarchaeota. Furthermore, phylogenetic analysis of the m7G capping pathway indicates that eukaryotic nuclei and Mimiviridae obtained this pathway from a common ancestral source that predated the origin of LECA. These results support the VE hypothesis and suggest the eukaryotic nucleus and the Mimiviridae descend from a common First Eukaryotic Nuclear Ancestor (FENA).

scholarly journals Comparative population genomic analyses of transporters within the Asgard archaeal superphylum

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247806
Author(s):  
Steven Russum ◽  
Katie Jing Kay Lam ◽  
Nicholas Alan Wong ◽  
Vasu Iddamsetty ◽  
Kevin J. Hendargo ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Life Forms ◽  
Transport Systems ◽  
Metabolic Potential ◽  
Atp Production ◽  
Archaeal Species ◽  
Evolution Of Life ◽  
Alignment Coverage ◽  
Secondary Carriers ◽  
Archaeal Ancestor

Upon discovery of the first archaeal species in the 1970s, life has been subdivided into three domains: Eukarya, Archaea, and Bacteria. However, the organization of the three-domain tree of life has been challenged following the discovery of archaeal lineages such as the TACK and Asgard superphyla. The Asgard Superphylum has emerged as the closest archaeal ancestor to eukaryotes, potentially improving our understanding of the evolution of life forms. We characterized the transportomes and their substrates within four metagenome-assembled genomes (MAGs), that is, Odin-, Thor-, Heimdall- and Loki-archaeota as well as the fully sequenced genome of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 that belongs to the Loki phylum. Using the Transporter Classification Database (TCDB) as reference, candidate transporters encoded within the proteomes were identified based on sequence similarity, alignment coverage, compatibility of hydropathy profiles, TMS topologies and shared domains. Identified transport systems were compared within the Asgard superphylum as well as within dissimilar eukaryotic, archaeal and bacterial organisms. From these analyses, we infer that Asgard organisms rely mostly on the transport of substrates driven by the proton motive force (pmf), the proton electrochemical gradient which then can be used for ATP production and to drive the activities of secondary carriers. The results indicate that Asgard archaea depend heavily on the uptake of organic molecules such as lipid precursors, amino acids and their derivatives, and sugars and their derivatives. Overall, the majority of the transporters identified are more similar to prokaryotic transporters than eukaryotic systems although several instances of the reverse were documented. Taken together, the results support the previous suggestions that the Asgard superphylum includes organisms that are largely mixotrophic and anaerobic but more clearly define their metabolic potential while providing evidence regarding their relatedness to eukaryotes.

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