scholarly journals Isolation of an archaeon at the prokaryote-eukaryote interface

2019 ◽  
Author(s):  
Hiroyuki Imachi ◽  
Masaru K. Nobu ◽  
Nozomi Nakahara ◽  
Yuki Morono ◽  
Miyuki Ogawara ◽  
...  
Keyword(s):  
Amino Acids ◽  
Marine Sediment ◽  
Current Data ◽  
Evolutionary Transition ◽  
Genomic Features ◽  
Morphological Complexity ◽  
Archaeal Lineage ◽  
Slow Growing ◽  
Origin Of Eukaryotes

AbstractThe origin of eukaryotes remains enigmatic. Current data suggests that eukaryotes may have risen from an archaeal lineage known as “Asgard archaea”. Despite the eukaryote-like genomic features found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear due to the lack of cultured representatives and corresponding physiological insight. Here we report the decade-long isolation of a Lokiarchaeota-related Asgard archaeon from deep marine sediment. The archaeon, “Candidatus Prometheoarchaeum syntrophicum strain MK-D1”, is an anaerobic, extremely slow-growing, small cocci (∼550 nm), that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexities have been proposed for Asgard archaea, the isolate has no visible organella-like structure. Ca. P. syntrophicum instead displays morphological complexity – unique long, and often, branching protrusions. Based on cultivation and genomics, we propose an “Entangle-Engulf-Enslave (E3) model” for eukaryogenesis through archaea-alphaproteobacteria symbiosis mediated by the physical complexities and metabolic dependency of the hosting archaeon.

scholarly journals Isolation of an archaeon at the prokaryote–eukaryote interface

Nature ◽  
2020 ◽  
Vol 577 (7791) ◽  
pp. 519-525 ◽  
Author(s):  
Hiroyuki Imachi ◽  
Masaru K. Nobu ◽  
Nozomi Nakahara ◽  
Yuki Morono ◽  
Miyuki Ogawara ◽  
...  
Keyword(s):  
Amino Acids ◽  
Marine Sediment ◽  
Current Data ◽  
Evolutionary Transition ◽  
Hypothetical Model ◽  
Genomic Features ◽  
Archaeal Lineage ◽  
Slow Growing ◽  
Origin Of Eukaryotes

Abstract The origin of eukaryotes remains unclear1–4. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as ‘Asgard’ archaea5,6. Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon—‘Candidatus Prometheoarchaeum syntrophicum’ strain MK-D1—is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea6, the isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle–engulf–endogenize (also known as E3) model.

From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell

2013 ◽  
Vol 41 (1) ◽  
pp. 451-457 ◽  
Author(s):  
Joran Martijn ◽  
Thijs J.G. Ettema
Keyword(s):  
Eukaryotic Cell ◽  
Convincing Evidence ◽  
Evolutionary Transition ◽  
Fusion Event ◽  
Genomic Features ◽  
Archaeal Lineage ◽  
Complex Features ◽  
Cellular Fusion ◽  
Origin Of Eukaryotes ◽  
Archaeal Ancestor

The evolutionary origin of the eukaryotic cell represents an enigmatic, yet largely incomplete, puzzle. Several mutually incompatible scenarios have been proposed to explain how the eukaryotic domain of life could have emerged. To date, convincing evidence for these scenarios in the form of intermediate stages of the proposed eukaryogenesis trajectories is lacking, presenting the emergence of the complex features of the eukaryotic cell as an evolutionary deus ex machina. However, recent advances in the field of phylogenomics have started to lend support for a model that places a cellular fusion event at the basis of the origin of eukaryotes (symbiogenesis), involving the merger of an as yet unknown archaeal lineage that most probably belongs to the recently proposed ‘TACK superphylum’ (comprising Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota) with an alphaproteobacterium (the protomitochondrion). Interestingly, an increasing number of so-called ESPs (eukaryotic signature proteins) is being discovered in recently sequenced archaeal genomes, indicating that the archaeal ancestor of the eukaryotic cell might have been more eukaryotic in nature than presumed previously, and might, for example, have comprised primitive phagocytotic capabilities. In the present paper, we review the evolutionary transition from archaeon to eukaryote, and propose a new model for the emergence of the eukaryotic cell, the ‘PhAT (phagocytosing archaeon theory)’, which explains the emergence of the cellular and genomic features of eukaryotes in the light of a transiently complex phagocytosing archaeon.

scholarly journals Growth performance and accretion of selected amino acids in response to three levels of dietary lysine fed to fast- and slow-growing broilers

2021 ◽  
Vol 100 (4) ◽  
pp. 100998
Author(s):  
D.H. Tran ◽  
J. Th. Schonewille ◽  
C. Pukkung ◽  
S. Khempaka
Keyword(s):  
Amino Acids ◽  
Growth Performance ◽  
Slow Growing

scholarly journals Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment

2020 ◽  
Author(s):  
Claus Pelikan ◽  
Kenneth Wasmund ◽  
Clemens Glombitza ◽  
Bela Hausmann ◽  
Craig W. Herbold ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Marine Sediment ◽  
Volatile Fatty Acids ◽  
Degradation Products ◽  
Stable Isotope Probing ◽  
Bacterial Degradation ◽  
Rrna Gene ◽  
Genomic Features ◽  
Carbon Processing

AbstractMicroorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet the taxonomic identities of microorganisms that actively degrade them remain poorly resolved. Here, we revealed identities, trophic interactions, and genomic features of bacteria that degraded 13C-labeled proteins and lipids in cold anoxic microcosms containing sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within 5 days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed 13C-labeling of various Deltaproteobacteria within 10 days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas species are prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides new insights into the identities, functions, and genomes of bacteria that actively degrade abundant necromass macromolecules in the seafloor.

Stereochemistry of amino acids in surface samples of a marine sediment

1978 ◽  
Vol 42 (12) ◽  
pp. 1903-1905 ◽  
Author(s):  
Glenn E. Pollock ◽  
Keith A. Kvenvolden
Keyword(s):  
Amino Acids ◽  
Marine Sediment ◽  
Surface Samples

scholarly journals The first peptides: The evolutionary transition between prebiotic amino acids and early proteins

2009 ◽  
Vol 261 (4) ◽  
pp. 531-539 ◽  
Author(s):  
Peter van der Gulik ◽  
Serge Massar ◽  
Dimitri Gilis ◽  
Harry Buhrman ◽  
Marianne Rooman
Keyword(s):  
Amino Acids ◽  
Evolutionary Transition ◽  
Early Proteins ◽  
Prebiotic Amino Acids

scholarly journals Anaerobic microbial degradation of protein and lipid macromolecules in subarctic marine sediment

2020 ◽  
Author(s):  
Claus Pelikan ◽  
Kenneth Wasmund ◽  
Clemens Glombitza ◽  
Bela Hausmann ◽  
Craig W. Herbold ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Marine Sediment ◽  
Volatile Fatty Acids ◽  
Degradation Products ◽  
Stable Isotope Probing ◽  
Rrna Gene ◽  
Genomic Features ◽  
Carbon Processing ◽  
Functional Partitioning

AbstractMicroorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet microorganisms that degrade them remain understudied. Here, we revealed identities, trophic interactions and genomic features of microorganisms that degraded 13C-labelled proteins and lipids in cold anoxic microcosms with sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within five days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed 13C-labeling of various Deltaproteobacteria within ten days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas were prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides an improved understanding of the metabolic processes and functional partitioning of necromass macromolecules among microorganisms in the seafloor.

scholarly journals Expanded Asgard archaea shed new light on the origin of eukaryotes and support a 2-domain tree of life

2021 ◽  
Author(s):  
Ruize Xie ◽  
Yinzhao Wang ◽  
Danyue Huang ◽  
Jialin Hou ◽  
Liuyang Li ◽  
...  
Keyword(s):  
Amino Acids ◽  
Carbon Fixation ◽  
Sister Group ◽  
Tree Of Life ◽  
Metabolic Reconstruction ◽  
Ecological Functions ◽  
Host Lineage ◽  
Phylogenomic Analyses ◽  
The Relationship ◽  
Origin Of Eukaryotes

AbstractThe hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. At present, only seven phyla are described in the Asgard superphylum, which limits our understanding of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of Asgard archaea. Here, we describe five novel phylum-level Asgard archaeal lineages, tentatively named Tyr-, Sigyn-, Freyr-, Hoder- and Balderarchaeota. Comprehensive phylogenomic analyses supported a new Asgard lineage Tyrarchaeota was identified as a deeper branching lineage cluster with the eukaryotic nuclear host lineage than Heimdallarchaeota that were previously considered as the closest archaeal relatives of eukaryotes. Metabolic reconstruction of Tyrarchaeota suggests a mixotrophic lifestyle of this archaea, capable of peptides and amino acids utilization while having the potential using the Wood-Ljungdahl pathway for carbon fixation and acetogenesis. This study largely expands the Asgard superphylum, provides additional evidences to support the 2-domain life tree thus sheds new light on the evolution and geochemical functions of the Asgard archaea.

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