Error propagation across levels of organization: From chemical stability of ribosomal RNA to developmental stability

Seligmann, Hervé

doi:10.1016/j.jtbi.2006.02.004

Cited by 25 publications

(10 citation statements)

References 88 publications

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“…Among the normalized distributions, 32 of 40 chains (80%) with a charge per atom >0.023 are either ribosomal or bind to ribosomes, and 25 of 42 chains (59%) with dipole per atom values >2.0 D interact with nucleic acids. In this context, Seligmann (18) suggests that dipole moments might explain substitution frequencies of nucleotides of genes coding for the corresponding proteins. Furthermore, it has been suggested that the dipole moments of helices may line up approximately along the gradients of the local electric fields (19).…”

Section: Resultsmentioning

confidence: 99%

A server and database for dipole moments of proteins

Felder

Prilusky

Silman

et al. 2007

Nucleic Acids Research

185

208

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An Internet server at http://bip.weizmann.ac.il/dipol calculates the net charge, dipole moment and mean radius of any 3D protein structure or its constituent peptide chains, and displays the dipole vector superimposed on a ribbon backbone of the protein. The server can also display the angle between the dipole and a selected list of amino acid residues in the protein. When the net charges and dipole moments of ∼12 000 non-homologous PDB biological units (PISCES set), and their unique chains of length 50 residues or longer, were examined, the great majority of both charges and dipoles fell into a very narrow range of values, with long extended tails containing a few extreme outliers. In general, there is no obvious relation between a protein's charge or dipole moment and its structure or function, so that its electrostatic properties are highly specific to the particular protein, except that the majority of chains with very large positive charges or dipoles bind to ribosomes or interact with nucleic acids.

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Section: Resultsmentioning

confidence: 99%

A server and database for dipole moments of proteins

Felder

Prilusky

Silman

et al. 2007

Nucleic Acids Research

185

208

View full text Add to dashboard Cite

show abstract

“…A model based on dipole moments of nucleotides suggests that substitution frequencies of nucleotides are proportional to the decrease in the dipole moment due to the substitution, where the general tendency is that nucleotides with high dipole moment tend to be replaced by nucleotides with low dipole moments [45]. This simplistic hypothesis is purely physico-chemical and would reflect only spontaneous forces affecting DNA contents.…”

Section: Transcriptional Versus Replicational Gradients: Mutation Ratesmentioning

confidence: 99%

Coding Constraints Modulate Chemically Spontaneous Mutational Replication Gradients in Mitochondrial Genomes

Seligmann

2012

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Distances from heavy and light strand replication origins determine duration mitochondrial DNA remains singlestranded during replication. Hydrolytic deaminations from A->G and C->T occur more on single- than doublestranded DNA. Corresponding replicational nucleotide gradients exist across mitochondrial genomes, most at 3rd, least 2nd codon positions. DNA singlestrandedness during RNA transcription causes gradients mainly in long-lived species with relatively slow metabolism (high transcription/replication ratios). Third codon nucleotide contents, evolutionary results of mutation cumulation, follow replicational, not transcriptional gradients in Homo; observed human mutations follow transcriptional gradients. Synonymous third codon position transitions potentially alter adaptive off frame information. No mutational gradients occur at synonymous positions forming off frame stops (these adaptively stop early accidental frameshifted protein synthesis), nor in regions coding for putative overlapping genes according to an overlapping genetic code reassigning stop codons to amino acids. Deviation of 3rd codon nucleotide contents from deamination gradients increases with coding importance of main frame 3rd codon positions in overlapping genes (greatest if these are 2nd position in overlapping genes). Third codon position deamination gradients calculated separately for each codon family are strongest where synonymous transitions are rarely pathogenic; weakest where transitions are frequently pathogenic. Synonymous mutations affect translational accuracy, such as error compensation of misloaded tRNAs by codon-anticodon mismatches (prevents amino acid misinsertion despite tRNA misacylation), a potential cause of pathogenic mutations at synonymous codon positions. Indeed, codon-family-specific gradients are inversely proportional to error compensation associated with gradient-promoted transitions. Deamination gradients reflect spontaneous chemical reactions in singlestranded DNA, but functional coding constraints modulate gradients.

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“…This exemplifies that developmental instability correlates with low fitness (Moller, 1997(Moller, , 1999. Apparently, in lizards, FA is negatively correlated with the accuracy of molecular processes, at least those in mitochondria (ribosomal chemical stability : Seligmann, 2006; structural stability of replication origins: Seligmann & Krishnan, 2006). However, the causal link between molecular instability and tail loss remains speculative.…”

Section: Tail-losers and Tail-retainersmentioning

confidence: 95%

Morphological, functional and evolutionary aspects of tail autotomy and regeneration in the ‘living fossil’Sphenodon (Reptilia: Rhynchocephalia)

Seligmann

Moravec

Werner

2008

Biological Journal of the Linnean Society

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Tail autotomy and regeneration are less known in Sphenodon ('Reptilia': Rhynchocephalia) than in Squamata. We examined museum specimens, Sphenodon guntheri (N = 8) and Sphenodon punctatus (N = 172), wild Sphenodon punctatus (N = 19) and Sphenodon sp. skeletons (N = 8). In S. punctatus, unlike in typical Squamata, sexes had similar relative (intact) tail lengths, and regeneration frequencies; tail and body growth was isometric. Tail breakage was usually intravertebral, usually followed by ablation of a variably sized terminal vertebral piece, partly deviating from lizards. Hypothetically, imperfect autotomy results from sphenodon's primitiveness. As in squamates, tail-losers were morphologically more left-side dominant than tail-retainers. Individual directional asymmetries in digit morphology and in digit injury were correlated (in lizards observed only at population level); tail-losers had more fluctuating asymmetry but their exclusion did not facilitate morphological taxonomic distinctions (no 'Seligmann effect'). In S. punctatus, extents and directions of sexual dimorphism paralleled differences between tail-retainers and tail-losers, females resembling tail-losers, also accounting for character interdependence (developmental constraints; employing a method similar to phylogenetic contrasts). The variation in the location of tail injury was correlated with the continuum of variation between injured and intact (pholidotic) morphotypes. These last two phenomena remain to be explored in Squamates.

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Error propagation across levels of organization: From chemical stability of ribosomal RNA to developmental stability

Cited by 25 publications

References 88 publications

A server and database for dipole moments of proteins

A server and database for dipole moments of proteins

Coding Constraints Modulate Chemically Spontaneous Mutational Replication Gradients in Mitochondrial Genomes

Morphological, functional and evolutionary aspects of tail autotomy and regeneration in the ‘living fossil’Sphenodon (Reptilia: Rhynchocephalia)

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