Isolation of an archaeon at the prokaryote–eukaryote interface
Hiroyuki Imachi,Masaru K. Nobu,Nozomi Nakahara,Nozomi Nakahara,Nozomi Nakahara,Yuki Morono,Miyuki Ogawara,Yoshihiro Takaki,Yoshinori Takano,Katsuyuki Uematsu,Tetsuro Ikuta,Motoo Ito,Yohei Matsui,Masayuki Miyazaki,Kazuyoshi Murata,Yumi Saito,Sanae Sakai,Chihong Song,Eiji Tasumi,Yuko Yamanaka,Takashi Yamaguchi,Yoichi Kamagata,Hideyuki Tamaki,Ken Takai,Ken Takai +24 more
TLDR
A hypothetical model for eukaryogenesis is proposed, termed the entangle–engulf–endogenize (also known as E 3 ) model, and isolation and characterization of an Asgard archaeon related to Lokiarchaeota reveals insights into how eukARYotes may have evolved from prokaryotes.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. Isolation and characterization of an archaeon that is most closely related to eukaryotes reveals insights into how eukaryotes may have evolved from prokaryotes.read more
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SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Journal ArticleDOI
Protein sequence analysis using the MPI Bioinformatics Toolkit
Felix Gabler,Seung-Zin Nam,Sebastian Till,Milot Mirdita,Martin Steinegger,Martin Steinegger,Johannes Söding,Andrei N. Lupas,Vikram Alva +8 more
TL;DR: Detailed information is provided on utilizing the three most widely accessed tools within the MPI Bioinformatics Toolkit: HHpred for the detection of homologs, HHpred in conjunction with MODELLER for structure prediction and homology modeling, and CLANS for the visualization of relationships in large sequence datasets.
Journal ArticleDOI
DRAM for distilling microbial metabolism to automate the curation of microbiome function
Michael Shaffer,Mikayla A. Borton,Bridget B. McGivern,Ahmed A. Zayed,Sabina Leanti La Rosa,Lindsey M. Solden,Pengfei Liu,Adrienne B. Narrowe,Josué Rodríguez-Ramos,Benjamin Bolduc,M. Consuelo Gazitúa,Rebecca A. Daly,Garrett J. Smith,Dean R. Vik,Phillip B. Pope,Matthew B. Sullivan,Simon Roux,Kelly C. Wrighton +17 more
TL;DR: DRAM (Distilled and Refined Annotation of Metabolism) is presented, a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits and provides critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.
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Diversity, ecology and evolution of Archaea
Brett J. Baker,Valerie De Anda,Kiley W. Seitz,Nina Dombrowski,Alyson E. Santoro,Karen G. Lloyd +5 more
TL;DR: How genomes belonging to uncultured groups from the environment elucidate the metabolic capabilities of the Archaea and their ecological roles are discussed, while also expanding the view of the tree of life and of eukaryogenesis.
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Innovations to culturing the uncultured microbial majority.
TL;DR: Common barriers that can hamper the isolation and culturing of novel microorganisms are discussed and emerging, innovative methods for targeted or high-throughput cultivation are reviewed.
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