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Liberles DA, Chang B, Geiler-Samerotte K, Goldman A, Hey J, Kaçar B, Meyer M, Murphy W, Posada D, Storfer A. Emerging Frontiers in the Study of Molecular Evolution. J Mol Evol 2020; 88:211-226. [PMID: 32060574 PMCID: PMC7386396 DOI: 10.1007/s00239-020-09932-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A collection of the editors of Journal of Molecular Evolution have gotten together to pose a set of key challenges and future directions for the field of molecular evolution. Topics include challenges and new directions in prebiotic chemistry and the RNA world, reconstruction of early cellular genomes and proteins, macromolecular and functional evolution, evolutionary cell biology, genome evolution, molecular evolutionary ecology, viral phylodynamics, theoretical population genomics, somatic cell molecular evolution, and directed evolution. While our effort is not meant to be exhaustive, it reflects research questions and problems in the field of molecular evolution that are exciting to our editors.
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Affiliation(s)
- David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
| | - Belinda Chang
- Department of Ecology and Evolutionary Biology and Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Kerry Geiler-Samerotte
- Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Aaron Goldman
- Department of Biology, Oberlin College and Conservatory, K123 Science Center, 119 Woodland Street, Oberlin, OH, 44074, USA
| | - Jody Hey
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Betül Kaçar
- Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michelle Meyer
- Department of Biology, Boston College, Chestnut Hill, MA, 02467, USA
| | - William Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - David Posada
- Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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Das S, Roymondal U, Sahoo S. Analyzing gene expression from relative codon usage bias in Yeast genome: a statistical significance and biological relevance. Gene 2009; 443:121-31. [PMID: 19410638 DOI: 10.1016/j.gene.2009.04.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2008] [Revised: 03/08/2009] [Accepted: 04/20/2009] [Indexed: 11/17/2022]
Abstract
Based on the hypothesis that highly expressed genes are often characterized by strong compositional bias in terms of codon usage, there are a number of measures currently in use that quantify codon usage bias in genes, and hence provide numerical indices to predict the expression levels of genes. With the recent advent of expression measure from the score of the relative codon usage bias (RCBS), we have explicitly tested the performance of this numerical measure to predict the gene expression level and illustrate this with an analysis of Yeast genomes. In contradiction with previous other studies, we observe a weak correlations between GC content and RCBS, but a selective pressure on the codon preferences in highly expressed genes. The assertion that the expression of a given gene depends on the score of relative codon usage bias (RCBS) is supported by the data. We further observe a strong correlation between RCBS and protein length indicating natural selection in favour of shorter genes to be expressed at higher level. We also attempt a statistical analysis to assess the strength of relative codon bias in genes as a guide to their likely expression level, suggesting a decrease of the informational entropy in the highly expressed genes.
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Affiliation(s)
- Shibsankar Das
- Department of Mathematics, Uluberia College, Uluberia, Howrah, W.B., India
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Egan JB, Jacobs ET, Martínez ME, Gerner EW, Jurutka PW, Thompson PA. Presence of a TA Haplotype in the APC Gene Containing the Common 1822 Polymorphism and Colorectal Adenoma. Cancer Res 2008; 68:6006-13. [DOI: 10.1158/0008-5472.can-08-1084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Laprevotte I. Scrambled duplications in the feline leukemia virus gag gene: a putative pattern for molecular evolution. J Mol Evol 1989; 29:135-48. [PMID: 2553988 DOI: 10.1007/bf02100112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The present study is a detailed computer-assisted analysis of the feline leukemia virus gag gene nucleotide sequence together with its flanking sequences (ST-FeLV GAG) that is compared with the aligned sectors of the Moloney strain of murine leukemia virus (Mo-MuLV GAG) and of three strains of feline sarcoma virus. It shows that perfectly matched repeated oligomers up to 13 nucleotides long are overrepresented and scattered throughout both ST-FeLV GAG and Mo-MuLV GAG, in noncoding and coding sectors, with no stringent correlation to codon usage in ST-FeLV gPr80gag. Many repeated oligomers share a core consensus that is intriguingly part of the inverted repeat at the termini of the long terminal repeat. Local scrambled repetitions of nucleotide subsequences have been found; they suggest a model of molecular evolution by slippage-like mechanisms. Thus, viral genomes could be subject to the same evolutionary mechanisms that are now known to be operating extensively in eukaryotic genomes. The data are discussed in light of putative patterns of molecular evolution.
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Affiliation(s)
- I Laprevotte
- Laboratoire d'Hématologie Expérimentale (CNRS), Centre Hayem, Hôpital Saint-Louis, Paris, France
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Frömmel C, Holzhütter HG. An estimate on the effect of point mutation and natural selection on the rate of amino acid replacement in proteins. J Mol Evol 1985; 21:233-57. [PMID: 6443130 DOI: 10.1007/bf02102357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We outline a method for estimating quantitatively the influence of point mutations and selection on the frequencies of codons and amino acids. We show how the mutation rate, i.e., the rate of amino acid replacement due to point mutation, can be affected by the codon usage as well as by the rates of the involved base exchanges. A comparison of the mutation rates calculated from reliable values of codon usage and base exchange probabilities with those that would be expected on the basis of chance reveals a notable suppression of replacements leading to tryptophan, glutamate, lysine, and methionine, and particularly of those leading to the termination codons. If selection constraints are neglected and only mutations are taken into account, the best agreement between expected and observed frequencies of both codons and amino acids is obtained for alpha = 1.13-1.15, where (Formula: see text). The "selection values" of codons and amino acids derived by our method show a pattern that partially deviates from others in the literature. For example, the selection pressure on methionine and cysteine turns out to be much more pronounced than expected if only the discrepancies between their observed and expected occurrences in proteins are considered. To estimate to what extent randomly occurring amino acid replacements are accepted by selection, we constructed an "acceptability matrix" from the well-established matrix of accepted point mutations. On the basis of this matrix "acceptability values" of the amino acids can be defined that correlate with their selection values. We also examine the significance of mutations and selection of amino acids with respect to their physicochemical properties and functions in proteins. The conservatism of amino acid replacements with respect to certain properties such as polarity can be brought about by the mutational process alone, whereas the conservatism with respect to other relevant properties--among them all measures of bulkiness--obviously is the result of additional selectional constraints on the evolution of protein structures.
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Horowitz H, Van Arsdell J, Platt T. Nucleotide sequence of the trpD and trpC genes of Salmonella typhimurium. J Mol Biol 1983; 169:775-97. [PMID: 6355484 DOI: 10.1016/s0022-2836(83)80136-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We have completed the nucleotide sequence determination of trpD and trpC, the second and third genes of the trp operon of Salmonella typhimurium. These genes encode two bifunctional proteins thought to have arisen by gene fusions: the trpD polypeptide contains the glutamine amido transferase and the phosphoribosyl anthranilate transferase activities, and the trpC protein possesses the N-(5'-phosphoribosyl)-anthranilic acid isomerase and the indole-3-glycerol phosphate synthetase activities. The trpD gene consists of 1593 nucleotides encoding 531 amino acids, and possesses an internal promoter (p2) located within a region from about 1400 to 1441 of the nucleotide sequence. The trpC gene contains 1356 nucleotides encoding 452 amino acids. In this paper we compare the trpD and trpC genes of S. typhimurium to those of Escherichia coli with respect to codon usage, nucleotide and amino acid conservation, p2 promoter characteristics and intercistronic regions. The sequence of the two genes we present here completes the sequence determination of the trp operon of S. typhimurium and should prove useful in comparisons with the E. coli trp operon and in future studies of operon structure in S. typhimurium.
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Smith MM, Andrésson OS. DNA sequences of yeast H3 and H4 histone genes from two non-allelic gene sets encode identical H3 and H4 proteins. J Mol Biol 1983; 169:663-90. [PMID: 6355483 DOI: 10.1016/s0022-2836(83)80164-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The complete DNA sequences of two loci encoding H3 and H4 histones in Saccharomyces cerevisiae have been determined. Each locus contains one H3 and one H4 gene. The genes at each locus are divergently transcribed and the coding sequences are separated by 646 base-pairs at one locus and 676 base-pairs at the other. The H3 genes code for identical histone H3 proteins and the H4 genes code for identical histone H4 proteins. The yeast proteins differ from histones H3 and H4 of calf by 15 and 8 amino acid substitutions, respectively, and these differences are largely confined to the carboxy-terminal halves of the proteins. The genes demonstrate a bias in synonymous codon usage similar to that noted for other yeast genes. This bias is confined to the coding sequences of the genes and is specific for the reading frame encoding the proteins. The coding sequence of each gene is flanked on both sides by DNA with an A + T content of 70 to 80%. Possible regulatory sequences are located relative to the 5' and 3'-termini of the histone H3 and H4 RNA transcripts.
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Golding GB, Strobeck C. Expected frequencies of codon use as a function of mutation rates and codon fitnesses. J Mol Evol 1982; 18:379-86. [PMID: 7175955 DOI: 10.1007/bf01840886] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A method is shown to determine the expected pattern of codon use for any given set of mutation rates between nucleotides and any set of fitnesses for the codons. If it is assumed that mutations to stop codons are lethal then those codons which can mutate in one step to a stop codon tend to be used less frequently. This tendency is however, a very small one and is not likely to be observable within a single gene. Nor is it necessarily a general tendency. For example, the leucine pretermination codons may be used preferentially when mutations to proline are deleterious. It is shown that different mutation rates (eg: transitions occurring more frequently than transversions) may have as large an effect on codon usage as would strong selection for particular codons. For the model presented, an increase in the rate of transitions strongly decreases the expected frequency of UGG and CRR codons. Other codes are moderately affected by such a change in the mutation rates. Many other models can be examined using this method.
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Nussinov R. RNA folding is unaffected by the nonrandom degenerate codon choice. BIOCHIMICA ET BIOPHYSICA ACTA 1982; 698:111-5. [PMID: 7126583 DOI: 10.1016/0167-4781(82)90125-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The frequent suggestion that the nonrandom codon usage is explained by its forming more stable mRNAs is tested in 22 genes. Only the histones, globins, and the rat preproinsulin gene show a correlation between the preferred degenerate codons and the stability of the secondary structure of the their mRNAs. However, the examined members from the histone and globin gene families, both among the oldest, in evolutionary sense, eukaryotic genes, have a high GC content (approx. 56% compared to an average of 42% in all eukaryotes) which is reflected in their degenerate codon choice and thus in their more stable folding.
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Horowitz H, Christie GE, Platt T. Nucleotide sequence of the trpD gene, encoding anthranilate synthetase component II of Escherichia coli. J Mol Biol 1982; 156:245-56. [PMID: 6283099 DOI: 10.1016/0022-2836(82)90326-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Aruja A, Vilu R, Raukas E. Detection of periodic patterns in RNA sequences: the first encapsidated region of the TMV RNA. J Theor Biol 1982; 94:457-70. [PMID: 7078214 DOI: 10.1016/0022-5193(82)90321-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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14
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Abstract
We present a method which permits comparison of the preferential use of degenerate codons within any gene. The method makes use of the triplet frequencies in the noncoding frames to assess whether a preference is specific to the reading frame. Preference is given a statistical meaning by use of the analysis of variance coupled to Duncan's multiple range test. Preferential use of degenerate codons is gene-specific and independent of gene size. The data suggest that any correlation between codon frequency distribution and tRNA levels is unreliable. In those animal genes examined, codons ending in C or G are preferred; in animal viruses tested, codons ending in U or A are preferred. Similarly, the bacterial genes and the genes of single-stranded DNA phages that we analyzed differed from each other as well as from eukaryotic genes in the third base of the codon.
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Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol 1981; 146:1-21. [PMID: 6167728 DOI: 10.1016/0022-2836(81)90363-6] [Citation(s) in RCA: 629] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Nichols BP, van Cleemput M, Yanofsky C. Nucleotide sequence of Escherichia coli trpE. Anthranilate synthetase component I contains no tryptophan residues. J Mol Biol 1981; 146:45-54. [PMID: 7021857 DOI: 10.1016/0022-2836(81)90365-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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17
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Nichols BP, Miozzari GF, van Cleemput M, Bennett GN, Yanofsky C. Nucleotide sequences of the trpG regions of Escherichia coli, Shigella dysenteriae, Salmonella typhimurium and Serratia marcescens. J Mol Biol 1980; 142:503-17. [PMID: 7007652 DOI: 10.1016/0022-2836(80)90260-0] [Citation(s) in RCA: 105] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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18
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Hasegawa M, Yasunaga T, Miyata T. Secondary structure of MS2 phage RNA and bias in code word usage. Nucleic Acids Res 1979; 7:2073-9. [PMID: 537920 PMCID: PMC342367 DOI: 10.1093/nar/7.7.2073] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Based on the secondary structural model of MS2 RNA, it is shown that, in base-pairing regions of the RNA, there is a bias in the use of synonymous codons which favours C and/or G over U and/or A in the third codon positions, and that in non-pairing regions, there is an opposite bias which favours U and/or A over C and/or G. This nature is interpreted as a result of selective constraint which stabilises the secondary structure of the single-stranded RNA genome of the MS2 phage.
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Sedlácek J, Fábry M, Rychlík I, Volný D, Vítek A. The arrangement of nucleotides in the coding regions of natural templates. MOLECULAR & GENERAL GENETICS : MGG 1979; 172:31-6. [PMID: 286872 DOI: 10.1007/bf00276212] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The relation of the nucleotide sequences in the coding regions of natural templates and of the short nucleotide sequence in 3' terminus of 16 S ribosomal RNA was found to differ from random pattern. The observation is interpreted in terms of both the ribosomal interactions and the molecular evolution.
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20
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Erickson JW, Altman GG. A search for patterns in the nucleotide sequence of the MS2 genome. J Math Biol 1979. [DOI: 10.1007/bf00275725] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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