…and RNA makes Protein. (part 2)

by Christoph — A two-part visual journey into the peptidyltransferase, where and how rRNA catalyzes ribosomal peptide-bond formation. Here is part 2...

smallthingsconsidered.blog

On the timing of eukaryotic origin

The emergence of eukaryotes marks a monumental juncture in the 4.6-billion-year evolutionary odyssey of our planet. Despite decades of research, the origin of eukaryotic life remains unresolved, with...

doi.org

Phylogenetic ancestry of Metamonada proteins points to a common origin of mitochondria in all eukaryotes

Abstract. Hypotheses concerning eukaryogenesis, the evolution of eukaryotic cells, differ in the relative timing of mitochondrial acquisition. Recently, a

dx.doi.org

Insertions in universal proteins confirm that Nanohaloarchaea belong to DPANN-Archaea and suggest several new major archaeal clades.

The phylogenetic position of Nanohaloarchaea has been debated, these nanosized archaea being alternatively proposed as sister group to Haloarchaea, members of the DPANN-Archaea, or sister group to Methanocellales. Screening a set of universal proteins, we identified four insertions located at critical locations in three ribosomal proteins and one RNA polymerase subunit that support the branching of Nanohaloarchaea as sister group to Aenigmarchaea within DPANN cluster II (sensu Dombrowski et al., 2020). Insertion analyses and phylogeny of the monomeric primase specific to DPANN-Archaea confirm the existence of a robust clade grouping Undinarchaea, Naiadarchaea and DPANN cluster II, that we propose to call Nanostetteria. Our insertion analysis also supports including Altiarchaea within DPANN-Archaea and suggest a new clades that has not been recovered in phylogenetic analyses, one grouping DPANN-Archaea with Stygia (Hadarchaea and relative) and an even large one grouping these lineages with Acherontia (Thermococci and relatives). The insertion defining this larger clade, present in the ribosomal protein uS7, is also present at the same position in Thaumarchaea, Korarchaea and a subgroup of Asgardarchaea. Whereas the insertion in Thaumarchaea is certainly due to an independent event, we discuss alternative hypotheses that can explain those present in Korarchaea and Asgardarchaea. Finally, we noticed several cases of MAGs misannotations, indicating that insertion analysis can be useful to identify protein with misleading affiliations. The existence of insertions in otherwise highly conserved universal proteins involved in translation or transcription could partly explain the high rate of protein evolution in some archaeal lineage, especially in DPANN-Archaea. ### Competing Interest Statement The authors have declared no competing interest.

biorxiv.org

Archaeal and eukaryotic MCM rings sequentially melt DNA for replication initiation - Nature Communications

To prepare for DNA replication, a short region of DNA base-pairs must be broken, termed melting, allowing a helicase to gain a foothold on an isolated DNA strand. Here, authors use single-particle cry...

doi.org

Chromatin organization in Asgard archaea: histones, SMC complexes, and the archaeal roots of eukaryotic chromatin

The genomes of organisms across the tree of life are structurally and functionally organized into chromatin. In eukaryotes, within an organelle called the nucleus, chromatin is shaped by histones and ...

cell.com

doi.org

A symbiotic origin of the ribosome?

Abstract. The origin of life is one of the great mysteries of science. Of the multiple unsolved problems, the origin of the translation system (the means b

academic.oup.com

A new family of rolling-circle replication endonucleases widespread in archaeal viruses and plasmids

Abstract. Archaea possess a remarkably diverse mobilome, but for many archaeal viruses and plasmids, even the basic processes, such as genome replication,

academic.oup.com

Archaeal family B DNA polymerase facilitates lagging strand DNA replication in the Thermococcales

Abstract. Replicative DNA synthesis is distributed among several DNA polymerases (DNAPs) in both Bacteria and Eukarya. The division of synthesis permits sp

academic.oup.com

Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome - Nature Communications

Bacterial genomes often include extrachromosomal replicons, ranging from small plasmids to chromosome-scale replicons. Here, Czarnecki et al. analyse more than 40,000 complete bacterial genomes and sh...

doi.org