Genotypes and Phenotypes in the Evolution of Molecules

Schuster, Peter

doi:10.1017/s1062798709000787

Cited by 11 publications

(9 citation statements)

References 120 publications

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“…This relationship ultimately encourages escape (evolvability) from constraints of order (stasis through structural canalization). Note that a large body of theoretical evidence supports these sequence-to-structure mappings and their consequences on the energetic and kinetic landscape of the evolving molecules [133,134]. Furthermore, some important predictions have already been confirmed experimentally in in vitro evolution of ribozymes [135].…”

Section: Methodsmentioning

confidence: 90%

The ancient history of the structure of ribonuclease P and the early origins of Archaea

Sun

Caetano‐Anollés

2010

BMC Bioinformatics

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BackgroundRibonuclease P is an ancient endonuclease that cleaves precursor tRNA and generally consists of a catalytic RNA subunit (RPR) and one or more proteins (RPPs). It represents an important macromolecular complex and model system that is universally distributed in life. Its putative origins have inspired fundamental hypotheses, including the proposal of an ancient RNA world.ResultsTo study the evolution of this complex, we constructed rooted phylogenetic trees of RPR molecules and substructures and estimated RPP age using a cladistic method that embeds structure directly into phylogenetic analysis. The general approach was used previously to study the evolution of tRNA, SINE RNA and 5S rRNA, the origins of metabolism, and the evolution and complexity of the protein world, and revealed here remarkable evolutionary patterns. Trees of molecules uncovered the tripartite nature of life and the early origin of archaeal RPRs. Trees of substructures showed molecules originated in stem P12 and were accessorized with a catalytic P1-P4 core structure before the first substructure was lost in Archaea. This core currently interacts with RPPs and ancient segments of the tRNA molecule. Finally, a census of protein domain structure in hundreds of genomes established RPPs appeared after the rise of metabolic enzymes at the onset of the protein world.ConclusionsThe study provides a detailed account of the history and early diversification of a fundamental ribonucleoprotein and offers further evidence in support of the existence of a tripartite organismal world that originated by the segregation of archaeal lineages from an ancient community of primordial organisms.

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Section: Methodsmentioning

confidence: 90%

The ancient history of the structure of ribonuclease P and the early origins of Archaea

Sun

Caetano‐Anollés

2010

BMC Bioinformatics

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“…The visualization incorporates the underlying LSH information in a visually intuitive manner to generate mutant spectra. When the differences in these plots resulting from altered selective pressures are visualized, they can represent projections of the hyperdimensional fitness landscape, if the frequency of the sequences has been demonstrated to correlate with phenotypic fitness (8). …”

Section: Discussionmentioning

confidence: 99%

“…These fitness landscapes have attracted considerable theoretical interest, but constructing them experimentally involves phenotypic analysis of all of alleles in the mutant spectrum, which can be technically challenging (7). In molecular evolution, the fitness landscape is a hyper-dimensional object with its dimensionality being a function of the length of the polymer in question (8). If one were able to generate a fitness landscapes for a sequence of interest under a variety of environmental conditions, these could be used to infer accessible evolutionary paths and even predict the course of evolution for that sequence.…”

Section: Introductionmentioning

confidence: 99%

SEWAL: an open-source platform for next-generation sequence analysis and visualization

Pitt

Rajapakse

Ferré-D′Amaré

2010

Nucleic Acids Research

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Next-generation DNA sequencing platforms provide exciting new possibilities for in vitro genetic analysis of functional nucleic acids. However, the size of the resulting data sets presents computational and analytical challenges. We present an open-source software package that employs a locality-sensitive hashing algorithm to enumerate all unique sequences in an entire Illumina sequencing run (∼108 sequences). The algorithm results in quasilinear time processing of entire Illumina lanes (∼107 sequences) on a desktop computer in minutes. To facilitate visual analysis of sequencing data, the software produces three-dimensional scatter plots similar in concept to Sewall Wright and John Maynard Smith’s adaptive or fitness landscape. The software also contains functions that are particularly useful for doped selections such as mutation frequency analysis, information content calculation, multivariate statistical functions (including principal component analysis), sequence distance metrics, sequence searches and sequence comparisons across multiple Illumina data sets. Source code, executable files and links to sample data sets are available at http://www.sourceforge.net/projects/sewal.

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“…Extensions of quasispecies theory to finite populations and changing environments (variable fitness landscapes (Chapter 5)) have been developed (Eigen, 2000;Wilke et al, 2001;Nowak, 2006;Saakian et al, , 2009Park et al, 2010;Schuster, 2010;; reviewed in Domingo, 2006;Domingo and Schuster, 2016). In the way virologists view quasispecies, a mutant distribution may be dominated by one or several master sequences whose preponderance may be transient or extended, dependent partly on environmental stability.…”

Section: Mutant Spectra Master Genomes and Consensus Sequencesmentioning

confidence: 99%

Darwinian Principles Acting on Highly Mutable Viruses

Domingo

2016

Virus as Populations

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Genotypes and Phenotypes in the Evolution of Molecules

Cited by 11 publications

References 120 publications

The ancient history of the structure of ribonuclease P and the early origins of Archaea

The ancient history of the structure of ribonuclease P and the early origins of Archaea

SEWAL: an open-source platform for next-generation sequence analysis and visualization

Darwinian Principles Acting on Highly Mutable Viruses

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