Abstract:
:RNA has a myriad of biological roles in contemporary life. We use the RNA paradigm for genotype-phenotype mappings to study the evolution of multiple coding in dependence to mutation rates. We study three different one-to-many genotype-phenotype mappings which have the potential to encode the information for multiple functions on a single sequence. These three different maps are (i) cofolding, where two sequences can bind and "cofold," (ii) suboptimal folding, where the alternative foldings within a certain range of the native state of sequences are considered, and (iii) adapter-based folding, in which protocells can evolve adapter-mediated alternative foldings. We study how protocells with a set of sequences can code for a set of predefined functional structures, while avoiding all other structures, which are considered to be misfoldings. Note that such misfolded structures are far more prevalent than functional ones. Our results highlight the flexibility of the RNA sequence to secondary structure mapping and the power of evolution to shape the genotype-phenotype mapping. We show that high fitness can be achieved even at high mutation rates. Mutation rates affect genome size, but differently depending on which folding method is used. We observe that cofolding limits the possibility to avoid misfolded structures and that adapters are always beneficial for fitness, but even more beneficial at low mutation rates. In all cases, the evolution procedure selects for molecules that can form additional structures. Our results indicate that inherent properties of RNA molecules and their interactions allow the evolution of complexity even at high mutation rates.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
de Boer FK,Hogeweg Pdoi
10.1007/s00239-014-9648-6subject
Has Abstractpub_date
2014-12-01 00:00:00pages
193-203issue
5-6eissn
0022-2844issn
1432-1432journal_volume
79pub_type
杂志文章abstract::Human endogenous retroviruses (HERVs) are the remnants of ancient germ cell infection by exogenous retroviruses and occupy up to 8% of the human genome. It has been suggested that HERV sequences have contributed to primate evolution by regulating the expression of cellular genes and mediating chromosome rearrangements...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-2656-1
更新日期:2004-11-01 00:00:00
abstract::The availability of fast and accurate sequencing procedures along with the use of PCR has led to a proliferation of studies of variability at the molecular level in populations. Nevertheless, it is often impractical to examine long genomic stretches and a large number of individuals at the same time. In order to optim...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00173194
更新日期:1995-12-01 00:00:00
abstract::Hypoxia at deep-sea hydrothermal vents represents one of the most basic challenges for metazoans, which then requires specific adaptations to acquire oxygen to meet their metabolic needs. Hydrothermal vent scale-worms (Polychaeta; Polynoidae) express large amounts of extracellular single- and multi-domain hemoglobins,...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-017-9815-7
更新日期:2017-12-01 00:00:00
abstract::We examined the nucleotide and amino acid sequence variation of the cytochrome c oxidase subunit II (COII) gene from 25 primates (4 hominoids, 8 Old World monkeys, 2 New World monkeys, 2 tarsiers, 7 lemuriforms, 2 lorisiforms). Marginal support was found for three phylogenetic conclusions: (1) sister-group relationshi...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00176084
更新日期:1994-03-01 00:00:00
abstract::This paper presents an essentially new method used to construct phylogenetic trees from related amino acid sequences. The method is based on a new distance measure which describes sequence relationships by means of typical steric and physicochemical properties of the amino acids and is advantageous in some essential p...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00160324
更新日期:1995-10-01 00:00:00
abstract::The size and diversity of bacteriophage populations require methodologies to quantitatively study the landscape of phage differences. Statistical approaches are confronted with small genome sizes forbidding significant single-phage analysis, and comparative methods analyzing full phage genomes represent an alternative...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-008-9068-6
更新日期:2008-03-01 00:00:00
abstract::The mitochondrial genetic variability in European rabbit (Oryctolagus cuniculus) populations present in Europe and North Africa from 11,000 years ago to the present day has been analyzed using ancient DNA techniques. DNA was extracted from 90 rabbit bones found in 22 archaeological sites dated between the Mesolithic a...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00163228
更新日期:1995-03-01 00:00:00
abstract::Recent experience with molecular phylogeny has shown that all molecular markers have strengths and weaknesses. Nonetheless, despite several notable discrepancies with phylogenies obtained from protein data, the merits of the small subunit ribosomal RNA (SSU rRNA) as a molecular phylogenetic marker remain indisputable....
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s002390010120
更新日期:2000-12-01 00:00:00
abstract::There is an 8/13 sequence match between actin and flagellin in their N-terminal regions. ...
journal_title:Journal of molecular evolution
pub_type: 信件
doi:10.1007/s00239-001-0067-0
更新日期:2002-02-01 00:00:00
abstract::Short interspersed DNA elements (SINEs) amplify by retroposition either by (i) successive waves of amplification from one or a few evolving master genes or by (ii) the generation of new master genes that coexist with their progenitors. Individual, highly conserved, elements of the B1 SINE family were identified from t...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s002390010087
更新日期:2000-09-01 00:00:00
abstract::Two competing effects at two vastly different scales may explain collagen's current translation length. The necessity to have long molecules for maintaining mechanical integrity at the organism and supraorganism scales may be limited by the need to have small molecules capable of robust self-assembly at the nanoscale....
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-008-9111-7
更新日期:2008-06-01 00:00:00
abstract::The diversity of functional genes and the related processes are important issues for conservation biology. This is especially relevant for populations that have suffered from demographic reduction as a consequence of the processes of postglacial colonization. In this perspective, the aims of the present study are (1) ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-011-9456-1
更新日期:2011-08-01 00:00:00
abstract::Variation in structure among primate hemoglobins is associated with variation in function. This supports the hypothesis that most substitutions observed among homologous proteins in different species have been fixed by natural selection because they contribute to the fitness of the genotype. It does not support the co...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01653958
更新日期:1972-12-01 00:00:00
abstract::Proteins are commonly used as molecular targets against pathogens such as viruses and bacteria. However, pathogens can evolve rapidly permitting their populations to increase in protein diversity over time and thus escape to the activity of a molecular therapy. Subsequently, in order to design more durable and robust ...
journal_title:Journal of molecular evolution
pub_type: 信件
doi:10.1007/s00239-020-09953-1
更新日期:2020-08-01 00:00:00
abstract::Friedreich ataxia is an autosomal recessive neurodegenerative disorder associated with a GAA repeat expansion in the first intron of the gene (FRDA) encoding a novel, highly conserved, 210 amino acid protein known as frataxin. Normal variation in repeat size was determined by analysis of more than 600 DNA samples from...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s002390010151
更新日期:2001-03-01 00:00:00
abstract::A major goal of evolutionary biology is to understand how beneficial mutations translate into increased fitness. Here, we study beneficial mutations that arise in experimental populations of yeast evolved in glucose-rich media. We find that fitness increases are caused by enhanced maximum growth rate (R) that come at ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-018-9829-9
更新日期:2018-02-01 00:00:00
abstract::Phylogenetic relationships among eight species of the Drosophila buzzatii species complex (D. mulleri subgroup; D. repleta species group) and D. hamatofila were determined by sequencing the mitochondrial cytochrome oxidase subunit I, II, and III genes. The species examined included members of the martensis cluster (D....
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00173155
更新日期:1995-12-01 00:00:00
abstract::The evolutionary relationships among arthropod hemocyanins and insect hexamerins were investigated. A multiple sequence alignment of 12 hemocyanin and 31 hexamerin subunits was constructed and used for studying sequence conservation and protein phylogeny. Although hexamerins and hemocyanins belong to a highly divergen...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006366
更新日期:1998-07-01 00:00:00
abstract::Studies so far have correlated the variation in the composition of snake venoms with the target prey population and snake's diet. Here we present the first example of an alternative evolutionary link between venom composition and dietary adaptation of snakes. We describe a dinucleotide deletion in the only three finge...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-0138-0
更新日期:2005-01-01 00:00:00
abstract::The finding that ribozymes can catalyze RNA chain elongation has led to the proposal that an early self-replicating system could have consisted of RNA alone. In such a chain elongation reaction, the Tetrahymena ribozyme was found to select 3',5'-linked substrates from a pool that contained a large molar excess of 2',5...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02602919
更新日期:1989-12-01 00:00:00
abstract::We characterized the organization of mitochondrial genes from a diverse range of hymenopterans. Of the 21 taxa characterized, 12 had distinct, derived organizations. Some rearrangements were consistent with the duplication-random loss mechanism, while others were not. Local inversions were relatively common, i.e., rea...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-002-2420-3
更新日期:2003-05-01 00:00:00
abstract::In vitro selection of Zn(2+)-dependent RNA-cleaving DNAzymes with activity at 90 degrees C has yielded a diverse spool of selected sequences. The RNA cleavage efficiency was found in all cases to be specific for Zn(2+) over Pb(2+), Ca(2+), Cd(2+), Co(2+), Hg(2+), and Mg(2+). The Zn(2+)-dependent activity assay of the ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-0374-3
更新日期:2005-08-01 00:00:00
abstract::The metabolic cycle of Saccharomyces cerevisiae consists of alternating oxidative (respiration) and reductive (glycolysis) energy-yielding reactions. The intracellular concentrations of amino acid precursors generated by these reactions oscillate accordingly, attaining maximal concentration during the middle of their ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-009-9218-5
更新日期:2009-05-01 00:00:00
abstract::While studies of the evolutionary histories of protein families are commonplace, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the nine spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely o...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-008-9149-6
更新日期:2008-12-01 00:00:00
abstract::Soluble lead salts and a number of lead-containing minerals catalyze the formation of oligonucleotides from nucleoside 5'-phosphorimidazolides. The effectiveness of lead compounds correlates strongly with their solubility. Under optimal conditions we were able to obtain 18% of pentamer and higher oligomers from ImpA. ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01732030
更新日期:1979-04-12 00:00:00
abstract::Male sex genes have shown a pattern of rapid interspecies divergence at both the coding and gene expression level. A common outcome from crosses between closely-related species is hybrid male sterility. Phenotypic and genetic studies in Drosophila sterile hybrid males have shown that spermatogenesis arrest is postmeio...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-010-9404-5
更新日期:2011-01-01 00:00:00
abstract::The codon assignment of the quasi-universal genetic code can be assumed to have resulted from the evolutionary pressures that prevailed when the code was still evolving. Here, we review studies of the structure of the genetic code based on optimization models. We also review studies that, from the structure of the cod...
journal_title:Journal of molecular evolution
pub_type: 杂志文章,评审
doi:10.1007/s00239-009-9287-5
更新日期:2009-11-01 00:00:00
abstract::Low oxygen and fluctuant ambient temperature pose serious challenges to mammalian survival. Physiological adaptations in mammals to hypoxia and low temperatures have been intensively investigated, yet their underlying molecular mechanisms need further exploration. Independent invasions of high-altitude plateaus, subte...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-018-9870-8
更新日期:2018-12-01 00:00:00
abstract::Circadian clock genes are remarkably conserved between eucoelomates. Although Drosophila has one copy of each major component, vertebrates have two or (in the case of the Period genes) three paralogs (Per1-3). We investigated the possibility that the vertebrate Per genes arose through two genome duplications during th...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-005-0185-1
更新日期:2006-06-01 00:00:00
abstract::We have identified and completely sequenced a novel plasmid isolated from the aphid Rhopalosiphum padi. Evidence which suggests that the plasmid occurs localized within the bacterial endosymbionts is presented. The plasmid contains the four genes that constitute the entire leucine operon. This fact makes it really uni...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00174042
更新日期:1995-07-01 00:00:00