Modern mRNA Proofreading and Repair: Clues that the Last Universal Common Ancestor Possessed an RNA Genome?

Poole, Anthony M.; Logan, D.T.

doi:10.1093/molbev/msi132

Cited by 73 publications

(63 citation statements)

References 115 publications

(121 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…However, it has now been experimentally established that molecular mechanisms for RNA repair exist in modern cells, as well as mechanisms to increase the fidelity of RNA synthesis. As stated by Poole and Logan in a recent review, ''This lends credibility to the proposal that the LUCA had an RNA genome'' (35).…”

Section: Corollariesmentioning

confidence: 70%

Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain

Forterre

2006

Proc. Natl. Acad. Sci. U.S.A.

217

175

View full text Add to dashboard Cite

The division of the living world into three cellular domains, Archaea, Bacteria, and Eukarya, is now generally accepted. However, there is no consensus about the evolutionary relationships among these domains, because all of the proposed models have a number of more or less severe pitfalls. Another drawback of current models for the universal tree of life is the exclusion of viruses, otherwise a major component of the biosphere. Recently, it was suggested that the transition from RNA to DNA genomes occurred in the viral world, and that cellular DNA and its replication machineries originated via transfers from DNA viruses to RNA cells. Here, I explore the possibility that three such independent transfers were at the origin of Archaea, Bacteria, and Eukarya, respectively. The reduction of evolutionary rates following the transition from RNA to DNA genomes would have stabilized the three canonical versions of proteins involved in translation, whereas the existence of three different founder DNA viruses explains why each domain has its specific DNA replication apparatus. In that model, plasmids can be viewed as transitional forms between DNA viruses and cellular chromosomes, and the formation of different levels of cellular organization (prokaryote or eukaryote) could be traced back to the nature of the founder DNA viruses and RNA cells.

show abstract

Section: Corollariesmentioning

confidence: 70%

Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain

Forterre

2006

Proc. Natl. Acad. Sci. U.S.A.

217

175

View full text Add to dashboard Cite

show abstract

“…92,93 The frequent presence of ribozymes in viroid, viroid-like satellite and HDV RNAs, strongly supports the view that they represent "living fossils" of an ancestral "RNA world". 94 Following the emergence of proteins and DNA, a common ancestor of Pol II and single-subunit RNA polymerases-predicted to catalyze replication of early RNA genomes 95,96 -presumably evolved to transcribe DNA templates. However, the initial ability to transcribe RNA templates may have been retained in present-day RNA polymerases, with the involvement of Pol II and NEP in the transcription of viroid and HDV RNAs representing the tip of an iceberg mostly composed by cellular RNAs.…”

Section: O N O T D I S T R I B U T Ementioning

confidence: 99%

Rolling-circle replication of viroids, viroid-like satellite RNAs and hepatitis delta virus: Variations on a theme

Flores¹,

Grubb²,

Elleuch³

et al. 2011

RNA Biology

113

View full text Add to dashboard Cite

“…Most researchers agree on the existence of an "RNA-Protein World" stage preceeding the divergence of Eubacteria, Archaea, and Eukarya, in which genetic information was stored in RNA [24,61,140,168,187]. Two competing theories postulate either a last common ancestor (LUCA) of the three domains with a DNA genome [13,109], or a LUCA with an RNA genome [41,55,61,89,133]. In the latter scenario, the transition to a DNA genomes occurred twice (once in Eubacteria and once in Archaea+Eukarya) [54] or even thrice [55], possibly mediated by viral entities.…”

Section: Origins Of Dna Genomesmentioning

confidence: 99%

Innovation in gene regulation: The case of chromatin computation

Prohaska

Stadler

Krakauer

2010

Journal of Theoretical Biology

View full text Add to dashboard Cite

Chromatin regulation is understood to be one of the fundamental modes of gene regulation in eukaryotic cells. We argue that the basic proteins that determine the chromatin architecture constitute an evolutionary ancient layer of transcriptional regulation common to all three domains of life. We explore phylogenetically, sources of innovation in chromatin regulation, focusing on protein domains related to chromatin structure and function, demonstrating a step-wise increase of complexity in chromatin regulation. Building upon the highly conserved use of variants of chromosomal architectural proteins to distinguish chromosomal states, Eukarya secondarily acquired mechanisms for "writing" chemical modifications onto chromatin that constitute persistent signals. The acquisition of reader domains enabled decoding of these complex, signal combinations and a decoupling of the signal from immediate biochemical effects. We show how the coupling of reading and writing, which is most prevalent in crown-group Eukarya, could have converted chromatin into a powerful computational device capable of storing and processing more information than pure cis-regulatory networks.Key words: Chromatin, gene regulation, evolution Summary of Findings and Evolutionary HypothesisGene regulation in extant organisms is a complex adaptive system making use of a diversity of mechanisms to ensure that proteins and complementary macromolecular components are produced and maintained at functional levels in variable environments.In this contribution we focus on one key regulatory subsystem of the cell: chromatin regulation. We argue that chromatin functioned as general regulator of transcription in the primordial nucleus, and that a series of key molecular innovations has significantly expanded the regulatory scope of the cell. In this section we summarize the key empirical results of the paper. Sections 2 through 6 provide the empirical support for these claims. In section 7, we formulate an evolutionary Email addresses: sonja@bioinf.uni-leipzig.de (Sonja J. Prohaska), studla@bioinf.uni-leipzig.de (Peter F. Stadler), krakauer@santafe.edu (David C. Krakauer) hypothesis that seeks to explain our findings in terms of the evolution of proto-genetic regulation. We then interpret this evolutionary sequence in terms of increasing computational power by locating key stages of the evolutionary sequence within a formal model of computation. Since sections 2-6 are primarily concerned with presenting evidence, those interested in the conceptual development of the argument can focus on sections 7 and 8.Two variants of Chromosomal Architectural Proteins (ChAPs) are sufficient to define binary genomic, and potentially phenotypic, states. We show how extensions to this binary system lead to potential distinctions among an increasing number of genomic states, culminating in forms of control localized to specific sites in the genome, as illustrated for example by extant mammalian histone variants capable of differential expression and/or localization to r...

show abstract

Modern mRNA Proofreading and Repair: Clues that the Last Universal Common Ancestor Possessed an RNA Genome?

Cited by 73 publications

References 115 publications

Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain

Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain

Rolling-circle replication of viroids, viroid-like satellite RNAs and hepatitis delta virus: Variations on a theme

Innovation in gene regulation: The case of chromatin computation

Contact Info

Product

Resources

About