scholarly journals Detecting adaptive convergent amino acid evolution

2019 ◽  
Vol 374 (1777) ◽  
pp. 20180234 ◽  
Author(s):  
Carine Rey ◽  
Vincent Lanore ◽  
Philippe Veber ◽  
Laurent Guéguen ◽  
Nicolas Lartillot ◽  
...  
Keyword(s):  
Amino Acid ◽  
Convergent Evolution ◽  
Evolutionary Genomics ◽  
Theme Issue ◽  
Coding Sequences ◽  
Difficult Question ◽  
Adaptive Processes ◽  
Definition Of

In evolutionary genomics, researchers have taken an interest in identifying substitutions that subtend convergent phenotypic adaptations. This is a difficult question that requires distinguishing foreground convergent substitutions that are involved in the convergent phenotype from background convergent substitutions. Those may be linked to other adaptations, may be neutral or may be the consequence of mutational biases. Furthermore, there is no generally accepted definition of convergent substitutions. Various methods that use different definitions have been proposed in the literature, resulting in different sets of candidate foreground convergent substitutions. In this article, we first describe the processes that can generate foreground convergent substitutions in coding sequences, separating adaptive from non-adaptive processes. Second, we review methods that have been proposed to detect foreground convergent substitutions in coding sequences and expose the assumptions that underlie them. Finally, we examine their power on simulations of convergent changes—including in the presence of a change in the efficacy of selection—and on empirical alignments. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions'.

scholarly journals Detecting convergent adaptive amino acid evolution

2019 ◽  
Author(s):  
Carine Rey ◽  
Vincent Lanore ◽  
Philippe Veber ◽  
Laurent Guéguen ◽  
Nicolas Lartillot ◽  
...  
Keyword(s):  
Amino Acid ◽  
Adaptive Evolution ◽  
Confounding Factor ◽  
Evolutionary Genomics ◽  
Phenotypic Evolution ◽  
Coding Sequences ◽  
Difficult Question

AbstractIn evolutionary genomics, researchers have taken an interest in identifying in the genomes substitutions that subtend convergent phenotypic adaptations. This is a difficult question to address, because genomes contain billions of sites, many of which have substituted in the lineages where the adaptations took place, and yet are not linked to them. Those extra substitutions may be linked to other adaptations, may be neutral, or may be linked to mutational biases. Furthermore, one can think of various ways of defining substitutions of interest, and various methods that match those definitions have been used, resulting in different sets of candidate substitutions. In this manuscript we first clarify how adaptation to convergent phenotypic evolution can manifest itself in coding sequences. Second, we review methods that have been proposed to detect convergent adaptive evolution in coding sequences and expose the assumptions that underlie them. Finally, we examine their power on simulations of convergent changes, including in the presence of a confounding factor.

scholarly journals Definition of the human raf amino-terminal regulatory region by deletion mutagenesis.

1989 ◽  
Vol 9 (2) ◽  
pp. 639-647 ◽  
Author(s):  
V P Stanton ◽  
D W Nichols ◽  
A P Laudano ◽  
G M Cooper
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Regulatory Region ◽  
Kinase Domain ◽  
Coding Sequences ◽  
Amino Terminal ◽  
Murine Sarcoma Virus ◽  
Transforming Activity ◽  
Definition Of ◽  
Initiation Sequence

Activation of transforming potential of the cellular raf gene has uniformly been associated with the deletion of amino-terminal coding sequences. In order to determine whether 5' truncation alone could activate cellular raf, we constructed 21 human c-raf-1 cDNAs with variable BAL 31-generated deletions distal to a Moloney murine sarcoma virus long terminal repeat and a consensus translation initiation sequence. The deletions ranged from 136 to 1,399 nucleotides of coding sequence and shortened the 648-amino-acid raf protein by 44 to 465 amino acids. The full-length c-raf-1 cDNA was nontransforming upon transfection of NIH 3T3 cells, as were four mutants with deletions of 142 or fewer amino acids. Seven of nine mutants with deletions of 154 to 273 amino acids induced transformation with efficiencies ranging from 0.25 to 70 foci per micrograms of DNA. Mutants with deletions of 303 to 324 amino acids displayed high transforming activities (comparable with that of v-raf), with a peak activity of 2,400 foci per microgram of DNA when 305 amino acids were deleted. Deletions of greater than 383 amino acids, extending into the raf kinase domain, lacked transforming activity. Northern (RNA) blotting and immunoprecipitation assays indicated that transfected NIH cells expressed raf RNAs and proteins of the expected sizes. Thus, 5' truncation alone can activate raf transforming potential, with a sharp peak of activation around amino acid 300. Analysis of three raf genes previously detected by transfection of tumor DNAs indicated that these genes were activated by recombination in raf intron 7 and encoded fusion proteins containing amino-terminal non-raf sequences. The extend of deletion of raf sequences in these recombinant genes corresponded to BAL 31 mutants which did not display high transforming activity, suggesting that the fused non-raf coding sequences may also contribute to biological activity.

scholarly journals Accurate detection of convergent amino-acid evolution with PCOC

2018 ◽  
Author(s):  
Carine Rey ◽  
Laurent Guéguen ◽  
Marie Sémon ◽  
Bastien Boussau
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Sensitivity And Specificity ◽  
Convergent Evolution ◽  
Amino Acid Position ◽  
Detection Methods ◽  
Protein Alignment ◽  
History Of ◽  
Definition Of ◽  
Genome Scale

AbstractIn the history of life, some phenotypes have been acquired several times independently, through convergent evolution. Recently, lots of genome-scale studies have been devoted to identify nucleotides or amino acids that changed in a convergent manner when the convergent phenotypes evolved. These efforts have had mixed results, probably because of differences in the detection methods, and because of conceptual differences about the definition of a convergent substitution. Some methods contend that substitutions are convergent only if they occur on all branches where the phenotype changed towards the exact same state at a given nucleotide or amino acid position. Others are much looser in their requirements and define a convergent substitution as one that leads the site at which they occur to prefer a phylogeny in which species with the convergent phenotype group together. Here we suggest to look for convergent shifts in amino acid preferences instead of convergent substitutions to the exact same amino acid. We define as convergent shifts substitutions that occur on all branches where the phenotype changed and such that they correspond to a change in the type of amino acid preferred at this position. We implement the corresponding model into a method named PCOC. We show on simulations that PCOC better recovers convergent shifts than existing methods in terms of sensitivity and specificity. We test it on a plant protein alignment where convergent evolution has been studied in detail and find that our method recovers several previously identified convergent substitutions and proposes credible new candidates.

Definition of the human raf amino-terminal regulatory region by deletion mutagenesis

1989 ◽  
Vol 9 (2) ◽  
pp. 639-647
Author(s):  
V P Stanton ◽  
D W Nichols ◽  
A P Laudano ◽  
G M Cooper
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Regulatory Region ◽  
Kinase Domain ◽  
Coding Sequences ◽  
Amino Terminal ◽  
Murine Sarcoma Virus ◽  
Transforming Activity ◽  
Definition Of ◽  
Initiation Sequence

Activation of transforming potential of the cellular raf gene has uniformly been associated with the deletion of amino-terminal coding sequences. In order to determine whether 5' truncation alone could activate cellular raf, we constructed 21 human c-raf-1 cDNAs with variable BAL 31-generated deletions distal to a Moloney murine sarcoma virus long terminal repeat and a consensus translation initiation sequence. The deletions ranged from 136 to 1,399 nucleotides of coding sequence and shortened the 648-amino-acid raf protein by 44 to 465 amino acids. The full-length c-raf-1 cDNA was nontransforming upon transfection of NIH 3T3 cells, as were four mutants with deletions of 142 or fewer amino acids. Seven of nine mutants with deletions of 154 to 273 amino acids induced transformation with efficiencies ranging from 0.25 to 70 foci per micrograms of DNA. Mutants with deletions of 303 to 324 amino acids displayed high transforming activities (comparable with that of v-raf), with a peak activity of 2,400 foci per microgram of DNA when 305 amino acids were deleted. Deletions of greater than 383 amino acids, extending into the raf kinase domain, lacked transforming activity. Northern (RNA) blotting and immunoprecipitation assays indicated that transfected NIH cells expressed raf RNAs and proteins of the expected sizes. Thus, 5' truncation alone can activate raf transforming potential, with a sharp peak of activation around amino acid 300. Analysis of three raf genes previously detected by transfection of tumor DNAs indicated that these genes were activated by recombination in raf intron 7 and encoded fusion proteins containing amino-terminal non-raf sequences. The extend of deletion of raf sequences in these recombinant genes corresponded to BAL 31 mutants which did not display high transforming activity, suggesting that the fused non-raf coding sequences may also contribute to biological activity.

scholarly journals Predictability in the evolution of Orthopteran cardenolide insensitivity

2019 ◽  
Vol 374 (1777) ◽  
pp. 20180246 ◽  
Author(s):  
Lu Yang ◽  
Nitin Ravikanthachari ◽  
Ricardo Mariño-Pérez ◽  
Riddhi Deshmukh ◽  
Mariana Wu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Convergent Evolution ◽  
Host Plants ◽  
Single Copy ◽  
Alpha Subunit ◽  
Herbivorous Insect ◽  
Amino Acid Substitutions ◽  
Theme Issue ◽  
Insect Order ◽  
The Family

The repeated evolutionary specialization of distantly related insects to cardenolide-containing host plants provides a stunning example of parallel adaptation. Hundreds of herbivorous insect species have independently evolved insensitivity to cardenolides, which are potent inhibitors of the alpha-subunit of Na + ,K + -ATPase (ATPα). Previous studies investigating ATPα-mediated cardenolide insensitivity in five insect orders have revealed remarkably high levels of parallelism in the evolution of this trait, including the frequent occurrence of parallel amino acid substitutions at two sites and recurrent episodes of duplication followed by neo-functionalization. Here we add data for a sixth insect order, Orthoptera, which includes an ancient group of highly aposematic cardenolide-sequestering grasshoppers in the family Pyrgomorphidae. We find that Orthopterans exhibit largely predictable patterns of evolution of insensitivity established by sampling other insect orders. Taken together the data lend further support to the proposal that negative pleiotropic constraints are a key determinant in the evolution of cardenolide insensitivity in insects. Furthermore, analysis of our expanded taxonomic survey implicates positive selection acting on site 111 of cardenolide-sequestering species with a single-copy of ATPα, and sites 115, 118 and 122 in lineages with neo-functionalized duplicate copies, all of which are sites of frequent parallel amino acid substitution. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.

scholarly journals THE EFFECT OF dl-METHIONINE, l-CYSTINE, AND dl-ISOLEUCINE ON THE UTILIZATION OF PARENTERALLY ADMINISTERED DOG HEMOGLOBIN

1947 ◽  
Vol 85 (1) ◽  
pp. 55-64 ◽  
Author(s):  
Leon L. Miller ◽  
Eric L. Alling
Keyword(s):  
Amino Acid ◽  
Developmental Stages ◽  
Peripheral Circulation ◽  
Amino Acid Mixture ◽  
Acid Mixture ◽  
Absorption Bands ◽  
Suggested Approach ◽  
Dog Plasma ◽  
Veronal Buffer ◽  
Definition Of

1. Further observations on the utilization of parenterally administered dog hemoglobin show that oral supplements of dl-methionine and l-cystine improve the efficiency of utilization of hemoglobin N, while a fed supplement of dl-isoleucine alone is without effect. 2. When N-isoleucine is added to a fed supplement of methionine or methionine and cystine, the utilization of parenterally given hemoglobin N is even better than with the sulfur-containing amino acids alone. 3. A suggested approach to the problem of designing the quantitatively "ideal" amino acid mixture lies in the definition of what may be called total organism-amino acid patterns of rat, dog, man, etc. These may vary considerably not only at different developmental stages in a given species, but also certainly from one species to another. 4. Further attempts to detect globin in the peripheral circulation have pointed to the need for a highly specific procedure such as that an immunologic method may offer. 5. Reduced hemin in dog plasma migrates with α1-globulin and albumin in veronal buffer at pH 8.5 and the colored zones give strong hemochromogen absorption bands.

scholarly journals How Does Replication-Associated Mutational Pressure Influence Amino Acid Composition of Proteins?

1999 ◽  
Vol 9 (5) ◽  
pp. 409-416 ◽  
Author(s):  
Pawel Mackiewicz ◽  
Agnieszka Gierlik ◽  
Maria Kowalczuk ◽  
Miroslaw R. Dudek ◽  
Stanislaw Cebrat
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Chromosome Replication ◽  
Amino Acid Substitutions ◽  
Mutational Pressure ◽  
Coding Sequences ◽  
Noncoding Sequences ◽  
Prokaryotic Genomes ◽  
Dna Strands

We have performed detrended DNA walks on whole prokaryotic genomes, on noncoding sequences and, separately, on each position in codons of coding sequences. Our method enables us to distinguish between the mutational pressure associated with replication and the mutational pressure associated with transcription and other mechanisms that introduce asymmetry into prokaryotic chromosomes. In many prokaryotic genomes, each component of mutational pressure affects coding sequences not only in silent positions but also in positions in which changes cause amino acid substitutions in coded proteins. Asymmetry in the silent positions of codons differentiates the rate of translation of mRNA produced from leading and lagging strands. Asymmetry in the amino acid composition of proteins resulting from replication-associated mutational pressure also corresponds to leading and lagging roles of DNA strands, whereas asymmetry connected with transcription and coding function corresponds to the distance of genes from the origin or terminus of chromosome replication.

scholarly journals Opinion on monoaminergic contributions to traits and temperament

2018 ◽  
Vol 373 (1744) ◽  
pp. 20170153 ◽  
Author(s):  
T. W. Robbins
Keyword(s):  
Neural Networks ◽  
Individual Differences ◽  
Social Functioning ◽  
Personality Factors ◽  
Monoamine Neurotransmitters ◽  
Neural Basis ◽  
Theme Issue ◽  
Experimental Animals ◽  
Neuroscience Research ◽  
Definition Of

This article critically reviews evidence relating temperamental traits and personality factors to the monoamine neurotransmitters, especially dopamine and serotonin. The genetic evidence is not yet considered to be conclusive and it is argued that basic neuroscience research on the neural basis of behaviour in experimental animals should be taken more into account. While questionnaire and lexical methodology including the ‘Five Factor’ theory has been informative (mostly for the traits relevant to social functioning, i.e. personality), biologically oriented approaches should be employed with more objective, theoretically grounded measures of cognition and behaviour, combined with neuroimaging and psychopharmacology, where appropriate. This strategy will enable specific functions of monoamines and other neuromodulators such as acetylcholine and neuropeptides (such as orexin) to be defined with respect to their roles in modulating activity in specific neural networks—leading to a more realistic definition of their interactive roles in complex, biologically based traits (i.e. temperament). This article is part of the theme issue ‘Diverse perspectives on diversity: multi-disciplinary approaches to taxonomies of individual differences’.

Direction of chromosome rearrangements in Saccharomyces cerevisiae by use of his3 recombinational substrates

1988 ◽  
Vol 8 (10) ◽  
pp. 4370-4380
Author(s):  
M T Fasullo ◽  
R W Davis
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Chromosomal Dna ◽  
Yeast Saccharomyces Cerevisiae ◽  
Coding Sequences ◽  
Mutant Strains ◽  
Genetic Techniques ◽  
Orthogonal Field ◽  
His3 Gene ◽  
Tandem Duplications

We used the his3 recombinational substrates (his3 fragments) to direct large interchromosomal (translocations) and intrachromosomal (deletions and tandem duplications) rearrangements in the yeast Saccharomyces cerevisiae. In strains completely deleted for the wild-type HIS3 gene, his3 fragments, one containing a deletion of 5' amino acid coding sequences and the other containing a deletion of 3' amino acid coding sequences, were first placed at preselected sites by homologous recombination. His+ revertants that arose via spontaneous mitotic recombination between the two his3 fragments were selected. This strategy was used to direct rearrangements in both RAD52+ and rad52 mutant strains. Translocations occurred in the RAD52+ genetic background and were characterized by orthogonal field alternating gel electrophoresis of yeast chromosomal DNA and by standard genetic techniques. An unexpected translocation was also identified in which HIS3 sequences were amplified. Two types of tandem duplications of the GAL(7, 10, 1) locus were also directed, and one type was not observed in rad52 mutants. Recombination mechanisms are discussed to account for these differences.

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