The last universal common ancestor between ancient Earth chemistry and the onset of genetics

Weiss, Madeline C.; Preiner, Martina; Zimorski, Verena; Martin, William

doi:10.1371/journal.pgen.1007518

Cited by 153 publications

(132 citation statements)

References 144 publications

(225 reference statements)

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“…It has been clear since 2004 that the strict core genome of all prokaryotes is extremely small. Only 14-30 genes were present in all of 147 diverse genomes (Charlebois and Doolittle 2004), and almost all of those genes encoded ribosomal proteins (Weiss et al 2018). However, it was still unexpected that the same would be true for a large collection of Streptococcus genomes.…”

Section: Effects Of Internal Annotations By Peppa Our Analyses Of 15mentioning

confidence: 99%

Accurate reconstruction of bacterial pan- and core- genomes with PEPPAN

Zhou

Charlesworth

Achtman

2020

Preprint

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Bacterial genomes have been shaped by a complex evolutionary history, including extensive homologous recombination, horizontal gene transfer, gene loss, and gene duplications. A pan-genome, consisting of all genes within a defined set of bacterial genomes, can provide the basis for phylogenetic inferences and population studies.Here we introduce PEPPA, a pipeline that can construct a pan-genome from thousands of genetically diversified bacterial genomes. PEPPA implements a combination of treeand synteny-based approaches to identify and exclude paralogous genes, which facilitates the ready construction of schemes for whole genome multi-locus sequence typing (wgMLST) and core genome MLST. PEPPA also implements similarity-based gene predictions that support consistent annotations of genes and pseudogenes in individual genomes, and which are nearly as accurate as expert manual curation. The PEPPA package includes PEPPA_parser, which calculates trees based on accessory gene content and MLST core genome allelic differences. We also present SimPan, a novel pipeline for simulating the evolution of a bacterial pan-genome. PEPPA was compared with four state-of-the-art pan-genome pipelines on both empirical and simulated datasets. It demonstrated greater accuracy and specificity than any other pipeline, and was almost as fast as any of them at calculating a pan-genome. To demonstrate its abilities, PEPPA was used to construct a Streptococcus pan-genome of >40,000 genes from 3,170 representative genomes spanning at least 80 species. The resulting gene and allelic trees provide an unprecedented overview of the genomic diversity of this genus. Kilian M, Poulsen K, Blomqvist T, Havarstein LS, Bek-Thomsen M, Tettelin H, Sorensen UB. 2008. Evolution of Streptococcus pneumoniae and its close commensal relatives. PLoS ONE 3: e2683. Kilian M and Tettelin H. 2019. Identification of virulence-associated properties by comparative genome analysis of Streptococcus pneumoniae, S. pseudopneumoniae, S. mitis, three S. oralis subspecies, and S. infantis. MBio 10. Konstantinidis KT, Rossello-Mora R, Amann R. 2017. Uncultivated microbes in need of their own taxonomy. ISME J 11: 2399-2406. Koonin EV. 2016. Splendor and misery of adaptation, or the importance of neutral null for understanding evolution. BMC Biol 14: 114.

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Section: Effects Of Internal Annotations By Peppa Our Analyses Of 15mentioning

confidence: 99%

Accurate reconstruction of bacterial pan- and core- genomes with PEPPAN

Zhou

Charlesworth

Achtman

2020

Preprint

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“…Central to the translation system, are the genes encoding the ribosomal RNA, the ribosomal proteins and associated factors, all of which ranked high in conservation and universality. Thus, the translational machinery was identified as one of the most ancient of systems in biology and was forming part of the core of the (hypothetical) Last Universal Common Ancestor (LUCA) (Gesteland and Atkins 1993;Woese 1998;Harris et al 2003;Charlebois and Doolittle 2004;Vetsigian et al 2006;Fournier et al 2010;Di Giulio 2011Hartman and Smith 2014;Bernier et al 2018;Weiss et al 2018;Coleman et al 2019).…”

Section: The 'Top-down' Approach-the Ribosome the Last Universal Commentioning

confidence: 99%

“…3A). Furthermore, it remains to be determined, whether the root is indeed placed between Archaea on one side and Bacteria on the other side or falls within Bacteria (Cavalier-Smith 2006;Lake et al 2009;Dagan et al 2010;, Weiss et al 2018. Finally, it is currently debated whether life should be divided into three major domains, i.e.…”

Section: The Importance Of a Rooted And Supported Tree Of Life For Unmentioning

confidence: 99%

The Emergence of Life

et al. 2019

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The aim of this article is to provide the reader with an overview of the different possible scenarios for the emergence of life, to critically assess them and, according to the conclusions we reach, to analyze whether similar processes could have been conducive to independent origins of life on the several icy moons of the Solar System. Instead of directly proposing a concrete and unequivocal cradle of life on Earth, we focus on describing the different requirements that are arguably needed for the transition between non-life to life. We Ocean Worlds Edited by 56 Page 2 of 53 E. Camprubí et al.approach this topic from geological, biological, and chemical perspectives with the aim of providing answers in an integrative manner. We reflect upon the most prominent origins hypotheses and assess whether they match the aforementioned abiogenic requirements. Based on the conclusions extracted, we address whether the conditions for abiogenesis are/were met in any of the oceanic icy moons.

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“…It is, however, not clear whether LUCA is a simple Archaea or Bacteria, or whether it is a more primitive organism, a Progenote [14,15,16,17,18]. For a recent review see [19]. But although LUCA, superficially looks rather simple, it is in fact very complicated and highly structured [17,19], and with all the fundamental preconditions for our life.…”

Section: Introductionmentioning

confidence: 99%

“…For a recent review see [19]. But although LUCA, superficially looks rather simple, it is in fact very complicated and highly structured [17,19], and with all the fundamental preconditions for our life. LUCA has a genetics and a metabolism controlled by enzymes in a cell with ion channels and active transport.…”

Section: Introductionmentioning

confidence: 99%

A Prerequisite for Life

Toxværd

2019

Journal of Theoretical Biology

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The complex physicochemical structures and chemical reactions in living organism have some common features: (1) The life processes take place in the cytosol in the cells, which, from a physicochemical point of view is an emulsion of biomolecules in a dilute aqueous suspension. (2) All living systems are homochiral with respect to the units of amino acids and carbohydrates, but (some) proteins are chiral unstable in the cytosol. (3) And living organism are mortal. These three common features together give a prerequisite for the prebiotic self-assembly at the start of the Abiogenesis. Here we argue , that it all together indicates, that the prebiotic self-assembly of structures and reactions took place in a more saline environment, whereby the homochirality of proteins not only could be obtained, but also preserved. A more saline environment for the prebiotic self-assembly of organic molecules and establishment of biochemical reactions could have been the hydrothermal vents.

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The last universal common ancestor between ancient Earth chemistry and the onset of genetics

Cited by 153 publications

References 144 publications

Accurate reconstruction of bacterial pan- and core- genomes with PEPPAN

Accurate reconstruction of bacterial pan- and core- genomes with PEPPAN

The Emergence of Life

A Prerequisite for Life

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