scholarly journals Nucleotide Sequence Evolution at the κ-Casein Locus: Evidence for Positive Selection Within the Family Bovidae

Genetics ◽  
1997 ◽  
Vol 147 (4) ◽  
pp. 1863-1872
Author(s):  
Todd J Ward ◽  
Rodney L Honeycutt ◽  
James N Derr
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Nucleotide Sequence ◽  
Positive Selection ◽  
Milk Protein ◽  
Nucleotide Substitution ◽  
Sequence Evolution ◽  
Amino Acid Sequence Level ◽  
Physiological Processes ◽  
The Family

Abstract κ-Casein is a mammalian milk protein involved in a number of important physiological processes. In the gut, the ingested protein is split into an insoluble peptide (para κ-casein) and a soluble hydrophilic glycopeptide (caseinomacropeptide). Caseinomacropeptide is responsible for increased efficiency of digestion, prevention of neonate hypersensitivity to ingested proteins, and inhibition of gastric pathogens. Variation within this peptide has significant effects associated with important traits such as milk production. The nucleotide sequences for regions of κ-casein exon and intron four were determined for representatives of the artiodactyl family Bovidae. The pattern of nucleotide substitution in κ-casein sequences for distantly related bovid taxa demonstrates that positive selection has accelerated their divergence at the amino acid sequence level. This selection has differentially influenced the molecular evolution of the two Kcasein split peptides and is focused within a 34-codon region of caseinomacropeptide.

scholarly journals Taxonomic status of Bhanja and Kismayo viruses (family Bunyaviridae)

2012 ◽  
Vol 17 (4) ◽  
pp. 4-8
Author(s):  
A. S Klimentov ◽  
A. P Gmyl ◽  
A. M Butenko ◽  
L. V Gmyl ◽  
O. V Isaeva ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Taxonomic Status ◽  
Amino Acid Sequences ◽  
The Family ◽  
L Segment

The nucleotide sequence of M= (1398 nucleotides and L= (6186 nucleotides) segments of the genome of Bhanja virus and L-segment (1297 nucleotides) of Kismayo virus has been partially determined. Phylogenetic analysis of deduced amino acid sequences showed that these viruses are novel members of the Flebovirus (Phlebovirus) genus in the family Bunyaviridae

scholarly journals Cloning and characterization of a second member of the mouse mdr gene family.

1988 ◽  
Vol 8 (7) ◽  
pp. 2770-2778 ◽  
Author(s):  
P Gros ◽  
M Raymond ◽  
J Bell ◽  
D Housman
Keyword(s):  
Multidrug Resistance ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Amino Acid Sequence ◽  
Gene Family ◽  
Predicted Amino Acid Sequence ◽  
Coding Region ◽  
Physiological Processes ◽  
Strong Homology ◽  
Energy Dependent

The mammalian mdr gene family comprises a small number of closely related genes. Previously, we have shown that one member, mdr1, has the capacity to convey multidrug resistance to drug-sensitive recipient cells in a gene transfer protocol. However, the functional characteristics of other members of this gene family have not been examined. In this report, we characterize a second member of the mdr gene family which we designated mdr2. We determined the nucleotide sequence corresponding to the complete coding region of this mdr2 transcript. The predicted amino acid sequence of this protein (1,276 amino acids) showed that it is a membrane glycoprotein highly homologous to mdr1 (85%), strongly suggesting that both genes originate from a common ancestor. Regions of divergence between mdr1 and mdr2 proteins are concentrated in two discrete segments of the predicted polypeptides, each approximately 100 residues in length. The mdr2 protein appears to be formed by the duplication of a structural unit which encodes three putative transmembrane loops and a predicted nucleotide-binding fold and is highly homologous to bacterial transport proteins such as hlyB. This strong homology suggests that mdr2 also participates in an energy-dependent membrane transport process. However, the direct relationship, if any, of this new member of the mdr family to multidrug resistance remains to be established. Knowledge of the complete nucleotide sequence and predicted amino acid sequence of the mdr2 gene product will enable the preparation of gene-specific probes and antibodies necessary to study the functional role of this gene in multidrug resistance and normal physiological processes.

scholarly journals The constraints between amino acids influence the unequal distribution of codons and protein sequence evolution

2021 ◽  
Vol 8 (6) ◽  
pp. 201852
Author(s):  
Yi Qian ◽  
Rui Zhang ◽  
Xinglu Jiang ◽  
Guoqiu Wu
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Molecular Evolution ◽  
Poisson Distribution ◽  
Protein Sequence ◽  
Sequence Evolution ◽  
Unequal Distribution ◽  
One Stop ◽  
Protein Sequence Evolution

Four nucleotides (A, U, C and G) constitute 64 codons at free combination but 64 codons are unequally assigned to 21 items (20 amino acids plus one stop). About 500 amino acids are known but only 20 are selected to make up the proteins. However, the relationships between amino acid and codon and between 20 amino acids have been unclear. In this paper, we studied the relationships between 20 amino acids in 33 species and found there were three constraints between 20 amino acids, such as the relatively stable mean carbon and hydrogen (C : H) ratios (0.50), similarity interactions between the constituent ratios of amino acids, and the frequency of amino acids according with Poisson distribution under certain conditions. We demonstrated that the unequal distribution of 64 codons and the choice of amino acids in molecular evolution would be constrained to remain stable C : H ratios. The constituent ratios and frequency of 20 amino acids in a species or a protein are two determinants of protein sequence evolution, so this finding showed the constraints between 20 amino acids played an important role in protein sequence evolution.

scholarly journals High Variability and Rapid Evolution of a Nanovirus

2010 ◽  
Vol 84 (18) ◽  
pp. 9105-9117 ◽  
Author(s):  
Ioana Grigoras ◽  
Tatiana Timchenko ◽  
Ana Grande-Pérez ◽  
Lina Katul ◽  
Heinrich-Josef Vetten ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Nucleotide Substitution ◽  
Rapid Evolution ◽  
Plant Viruses ◽  
High Variability ◽  
Nucleotide Substitution Rate ◽  
Virus Propagation ◽  
The Family ◽  
Leguminous Crops ◽  
Ssdna Viruses

ABSTRACT Nanoviruses are multipartite single-stranded DNA (ssDNA) plant viruses that cause important diseases of leguminous crops and banana. Little has been known about the variability and molecular evolution of these viruses. Here we report on the variability of faba bean necrotic stunt virus (FBNSV), a nanovirus from Ethiopia. We found mutation frequencies of 7.52 × 10−4 substitutions per nucleotide in a field population of the virus and 5.07 × 10−4 substitutions per nucleotide in a laboratory-maintained population derived thereof. Based on virus propagation for a period of more than 2 years, we determined a nucleotide substitution rate of 1.78 × 10−3 substitutions per nucleotide per year. This high molecular evolution rate places FBNSV, as a representative of the family Nanoviridae, among the fastest-evolving ssDNA viruses infecting plants or vertebrates.

scholarly journals Two decades of suspect evidence for adaptive molecular evolution - Negative selection confounding positive selection signals

2021 ◽  
Author(s):  
Qipian Chen ◽  
Hao Yang ◽  
Xiao Feng ◽  
Qingjian Chen ◽  
Suhua Shi ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Dna Sequences ◽  
Negative Selection ◽  
Genomic Sequence ◽  
Sequence Evolution ◽  
Mk Test ◽  
Random Expectation ◽  
Two Stages ◽  
Rule Out

There is a large literature in the last two decades affirming adaptive DNA sequences evolution between species. The main lines of evidence are from i) the McDonald-Kreitman (MK) test, which compares divergence and polymorphism data, and ii) the PAML test, which analyzes multi-species divergence data. Here, we apply these two tests concurrently on the genomic data of Drosophila and Arabidopsis. To our surprise, the >100 genes identified by the two tests do not overlap beyond random expectation. Because the non-concordance could be due to low powers leading to high false-negatives, we merge every 20 - 30 genes into a "supergene". At the supergene level, the power of detection is large but the calls still do not overlap. We rule out methodological reasons for the non-concordance. In particular, extensive simulations fail to find scenarios whereby positive selection can only be detected by either MK or PAML, but not both. Since molecular evolution is governed by positive and negative selection concurrently, a fundamental assumption for estimating one (say, positive selection) is that the other is constant. However, in a broad survey of primates, birds, Drosophila and Arabidopsis, we found that negative selection rarely stays constant for long in evolution. As a consequence, the variation in negative selection is often mis-construed as signals of positive selection. In conclusion, MK, PAML or any method that examines genomic sequence evolution has to explicitly address the variation in negative selection before estimating positive selection. In a companion study, we propose a possible path forward in two stages – first, by mapping out the changes in negative selection and then using this map to estimate positive selection. For now, the large literature on positive selection between species has to await the re-assessment.

scholarly journals Complete Nucleotide Sequence of a Partitivirus from Rhizoctonia solani AG-1 IA Strain C24

Viruses ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 703 ◽  
Author(s):  
Chen Liu ◽  
Miaolin Zeng ◽  
Meiling Zhang ◽  
Canwei Shu ◽  
Erxun Zhou
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Rhizoctonia Solani ◽  
Sheath Blight ◽  
Open Reading Frame ◽  
Rice Sheath Blight ◽  
Rna Dependent Rna Polymerase ◽  
Reading Frame ◽  
The Family

The complete genome of a novel double-stranded (ds) RNA mycovirus, named as Rhizoctonia solani partitivirus 5 (RsPV5), isolated from rice sheath blight fungus R. solani AG-1 IA strain C24, was sequenced and analysed. RsPV5 consists of two segments, dsRNA-1 (1899 nucleotides) and dsRNA-2 (1787 nucleotides). DsRNA-1 has an open reading frame (ORF) 1 that potentially codes for a protein of 584 amino acid (aa) containing the conserved motifs of a RNA-dependent RNA polymerase (RdRp), and dsRNA-2 also contains a ORF 2, encoding a putative capsid protein (CP) of 513 aa. Phylogenetic analysis revealed that RsPV5 clustered together with six other viruses in an independent clade of the genus Alphapartitivirus, indicating that RsPV5 was a new member of the genus Alphapartitivirus, within the family Partitiviridae.

scholarly journals Nucleotide Substitution and Recombination at Orthologous Loci in Staphylococcus aureus

2005 ◽  
Vol 187 (8) ◽  
pp. 2698-2704 ◽  
Author(s):  
Austin L. Hughes ◽  
Robert Friedman
Keyword(s):  
Staphylococcus Aureus ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Ribosomal Proteins ◽  
Nucleotide Substitution ◽  
Binding Protein ◽  
Amino Acid Sequence Level ◽  
Fibrinogen Binding ◽  
Genes Encoding ◽  
Orthologous Loci

ABSTRACT The pattern of nucleotide substitution was examined at 2,129 orthologous loci among five genomes of Staphylococcus aureus, which included two sister pairs of closely related genomes (MW2/MSSA476 and Mu50/N315) and the more distantly related MRSA252. A total of 108 loci were unusual in lacking any synonymous differences among the five genomes; most of these were short genes encoding proteins highly conserved at the amino acid sequence level (including many ribosomal proteins) or unknown predicted genes. In contrast, 45 genes were identified that showed anomalously high divergence at synonymous sites. The latter genes were evidently introduced by homologous recombination from distantly related genomes, and in many cases, the pattern of nucleotide substitution made it possible to reconstruct the most probable recombination event involved. These recombination events introduced genes encoding proteins that differed in amino acid sequence and thus potentially in function. Several of the proteins are known or likely to be involved in pathogenesis (e.g., staphylocoagulase, exotoxin, Ser-Asp fibrinogen-binding bone sialoprotein-binding protein, fibrinogen and keratin-10 binding surface-anchored protein, fibrinogen-binding protein ClfA, and enterotoxin P). Therefore, the results support the hypothesis that exchange of homologous genes among S. aureus genomes can play a role in the evolution of pathogenesis in this species.

scholarly journals Human thymidine kinase gene: molecular cloning and nucleotide sequence of a cDNA expressible in mammalian cells.

1984 ◽  
Vol 4 (11) ◽  
pp. 2316-2320 ◽  
Author(s):  
H D Bradshaw ◽  
P L Deininger
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Thymidine Kinase ◽  
Mammalian Cells ◽  
Simian Virus 40 ◽  
Thymidine Kinase Gene ◽  
Coding Region ◽  
Base Pairs ◽  
Amino Acid Sequence Level ◽  
Kinase Gene

A cDNA containing the entire coding region of the human thymidine kinase gene has been molecularly cloned. The cDNA is under the control of a simian virus 40 promoter and is expressible in mammalian cells. The complete nucleotide sequence of the human thymidine kinase cDNA has been determined. The cDNA is 1,421 base pairs in length and has a large open reading frame of 702 base pairs capable of specifying a protein with a molecular weight of 25,504. Genomic Southern blotting experiments show that sequences homologous to the human thymidine kinase cDNA are conserved among many vertebrates, including prosimians (lemur), tree shrews, rats, mice, and chickens. Direct comparison of the nucleotide sequences of the human thymidine kinase cDNA and the chicken thymidine kinase gene reveals ca. 70% overall homology. This homology is extended further at the amino acid sequence level, with greater than 74% amino acid residues matched between the human and chicken thymidine kinase proteins.

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