Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application

1980 ◽  
Vol 16 (1) ◽  
pp. 23-36 ◽  
Author(s):  
Takashi Miyata ◽  
Teruo Yasunaga
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Nucleotide Sequences ◽  
Evolutionary Rates ◽  
Amino Acid Substitutions

scholarly journals Molecular Evolution of β-Lactam-Resistant Haemophilus influenzae: 9-Year Surveillance of Penicillin-Binding Protein 3 Mutations in Isolates from Japan

2006 ◽  
Vol 50 (7) ◽  
pp. 2487-2492 ◽  
Author(s):  
Yumiko Sanbongi ◽  
Takahisa Suzuki ◽  
Yumi Osaki ◽  
Nami Senju ◽  
Takashi Ida ◽  
...  
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Haemophilus Influenzae ◽  
Clavulanic Acid ◽  
Antimicrobial Agents ◽  
Binding Protein ◽  
Amino Acid Substitutions ◽  
Penicillin Binding Protein ◽  
Amoxicillin Clavulanic Acid ◽  
Second Period

ABSTRACT A total of 621 clinical isolates of Haemophilus influenzae collected in Japan between 1995 and 2003 were studied for their susceptibilities to several antimicrobial agents, β-lactamase production, and amino acid substitutions in penicillin-binding protein 3 (PBP 3). Over the four study periods (first period, 1995 to 1996; second period, 1997 to 1998; third period, 2000 to 2001; fourth period, 2002 to 2003), the susceptibilities to β-lactam agents decreased and the incidence of isolates with substitutions at positions 377, 385, 389, 517, and/or 526 in PBP 3 increased from 28.8% to 52.0%. Five hundred seventy-one β-lactamase-nonproducing isolates were grouped into 18 classes, based on the pattern of the five mutations in PBP 3. The Asp526Lys substitution led to 6.0-, 4.3-, 2.4-, and 5.4-fold increases in amoxicillin-clavulanic acid, cefdinir, cefditoren, and faropenem resistance, respectively. PBP 3 with multiple substitutions (Met377Ile, Ser385Thr, and/or Leu389Phe) together with Asp526Lys resulted in increased resistance compared to that for PBP 3 with the Asp526Lys substitution alone. These results indicate that mutations at these five positions increased resistance to most β-lactams. Although a significant change in the prevalence of β-lactamase-producing strains was not observed, the proportions of those possessing both PBP 3 alterations and β-lactamase production have slightly increased (from 1.4% to 5.0%). The ROB-1 β-lactamase was rare, but this is the first report of this β-lactamase in Japan.

scholarly journals Computational Analysis of the Sequences of LIPE Gene of Selected Ruminants and Non-ruminants

2019 ◽  
pp. 1-10
Author(s):  
Rasheed B. Fatai ◽  
Mabel O. Akinyemi ◽  
Osamede Henry Osaiyuwu
Keyword(s):  
Amino Acid ◽  
Protein Kinase ◽  
Water Buffalo ◽  
Nucleotide Sequences ◽  
Molecular Techniques ◽  
Farm Animals ◽  
Mass Selection ◽  
Amino Acid Substitutions ◽  
Sequencing Analysis ◽  
Single Nucleotide

Tropically adapted farm animals are characterized by low meat and milk productivity. Traditionally, mass selection has been widely employed in breeding for improved animal performance. However, improving animal productivity using mass selection is laborious and usually less effective. Advances in molecular techniques such as DNA sequencing analysis provide the opportunity to characterize meat and milk influencing genes, which can lead to faster genetic improvement but often unaffordable and expensive particularly in developing countries. Unlike the wet laboratory analysis, computational molecular analyses is comparatively cheaper in pre-screening of the functional impacts of nonsynonymous single-nucleotide variants of some performance traits-related genes such as hormone-sensitive lipase (LIPE). A total of fifteen (15) LIPE nucleotide sequences comprising pig (3), cattle (3), water buffalo (2), camel (2), goat (2) and sheep (3) were retrieved from the Genbank. Also, twenty (20) functionally associated genes with the LIPE gene including perilipin 1, 2 & 5 protein kinase cAMP-activated catalytic subunit alpha, protein kinase X-linked were determined using the GeneMANIA. Functional analysis of non-synonymous single nucleotide polymorphism using PROVEAN showed that ten amino acid substitutions (S216C, P107del, Q28_P29insRATHVA, S41_S44dup, A640M, S940A, L660I,  D86delinsWA, S1000F) in water buffalo and pig (X678E, V789K, G987del, T218K, Q2234del, L278H, Q321del, L1023delinsPKL, P1452V, H1267delinsRFT), nine in sheep (F67_P68delinsVQ, R24G, A247_R248dup, L122L, L144P, S149K, S125S,  S224H, G148M) and goats (A450Y, P480H, G490delinsPHQ, L500R, R550del, S100_S101dup, E600S, A700Q, P754delinsQAW) and five in camel (A320A, S210S, L130L, T400T, L440I) were found neutral indicating their beneficial effect while only T110A out of the fifteen amino acid substitutions was found deleterious in cattle. The obtained phylogenetic trees from the nucleotide sequences showed a closer relationship among the members of the Bovidae family particularly the sheep and cattle. This information may aid future research that aims at the selection of the studied animals for improved meat and milk quality traits.

scholarly journals Enrichment in conservative amino acid changes among fixed and standing missense variations in slowly evolving proteins

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9983
Author(s):  
Mingrui Wang ◽  
Dapeng Wang ◽  
Jun Yu ◽  
Shi Huang
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Rhesus Macaques ◽  
Neutral Theory ◽  
Evolutionary Rates ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Project Data ◽  
The Impact

The process of molecular evolution has many elements that are not yet fully understood. Evolutionary rates are known to vary among protein coding and noncoding DNAs, and most of the observed changes in amino acid or nucleotide sequences are assumed to be non-adaptive by the neutral theory of molecular evolution. However, it remains unclear whether fixed and standing missense changes in slowly evolving proteins are more or less neutral compared to those in fast evolving genes. Here, based on the evolutionary rates as inferred from identity scores between orthologs in human and Rhesus Macaques (Macaca mulatta), we found that the fraction of conservative substitutions between species was significantly higher in their slowly evolving proteins. Similar results were obtained by using four different methods of scoring conservative substitutions, including three that remove the impact of substitution probability, where conservative changes require fewer mutations. We also examined the single nucleotide polymorphisms (SNPs) by using the 1000 Genomes Project data and found that missense SNPs in slowly evolving proteins also had a higher fraction of conservative changes, especially for common SNPs, consistent with more non-conservative substitutions and hence stronger natural selection for SNPs, particularly rare ones, in fast evolving proteins. These results suggest that fixed and standing missense variants in slowly evolving proteins are more likely to be neutral.

scholarly journals Mutational biases influence parallel adaptation

2017 ◽  
Author(s):  
Arlin Stoltzfus ◽  
David M. McCandlish
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Null Model ◽  
Mutation Rates ◽  
Amino Acid Substitutions

AbstractWhile mutational biases strongly influence neutral molecular evolution, the role of mutational biases in shaping the course of adaptation is less clear. Here we consider the frequency of transitions relative to transversions among adaptive substitutions. Because mutation rates for transitions are higher than those for transversions, if mutational biases influence the dynamics of adaptation, then transitions should be over-represented among documented adaptive substitutions. To test this hypothesis, we assembled a dataset of putatively adaptive amino acid substitutions that have occurred in parallel during evolution in nature or in the laboratory. We find that the frequency of transitions in this dataset is much higher than would be predicted under a null model where mutation has no effect. Our results are qualitatively similar even if we restrict ourself to changes that have occurred, not merely twice, but three or more times. These results suggest that the course of adaptation is biased by mutation.

The primary structure of carp myoglobin in the context of molecular evolution

1982 ◽  
Vol 297 (1084) ◽  
pp. 1-25 ◽  
Keyword(s):  
Skeletal Muscle ◽  
Amino Acid ◽  
Molecular Evolution ◽  
Amino Acid Sequence ◽  
Neutral Theory ◽  
Amino Acid Substitutions ◽  
Biochemical Evolution ◽  
Constant Rate ◽  
Rate Of Molecular Evolution ◽  
Living Species

The amino acid sequence of skeletal muscle myoglobin from carp ( Cyprinus carpio ) is presented. Comparisons are made with previously reported myoglobin sequences for several other fish and birds, and many mammals. The functional significance of the amino acid substitutions and ‘deletions’ in the carp sequence is considered. The new sequence is used in a re-examination of the evidence for an approximately constant rate of molecular evolution. By using estimates of the dates of divergence of lineages leading to living species and equations put forward by proponents of the ‘neutral theory’ of biochemical evolution it is demonstrated that similar amounts of change appear to have occurred over periods of time that differ by more than a factor of two.

Recombinant Variants of Tissue-Type Plasminogen Activator Containing Amino Acid Substitutions in the Finger Domain

1992 ◽  
Vol 68 (06) ◽  
pp. 672-677 ◽  
Author(s):  
Hitoshi Yahara ◽  
Keiji Matsumoto ◽  
Hiroyuki Maruyama ◽  
Tetsuya Nagaoka ◽  
Yasuhiro Ikenaka ◽  
...  
Keyword(s):  
Amino Acid ◽  
Plasminogen Activator ◽  
Half Life ◽  
Tissue Type ◽  
Clot Lysis ◽  
Amino Acid Substitutions ◽  
Wild Type ◽  
Plasma Clot ◽  
Tissue Type Plasminogen Activator ◽  
Type Plasminogen Activator

SummaryTissue-type plasminogen activator (t-PA) is a fibrin-specific agent which has been used to treat acute myocardial infarction. In an attempt to clarify the determinants for its rapid clearance in vivo and high affinity for fibrin clots, we produced five variants containing amino acid substitutions in the finger domain, at amino acid residues 7–9, 10–14, 15–19, 28–33, and 37–42. All the variants had a prolonged half-life and a decreased affinity for fibrin of various degrees. The 37–42 variant demonstrated about a 6-fold longer half-life with a lower affinity for fibrin. Human plasma clot lysis assay estimated the fibrinolytic activity of the 37–42 variant to be 1.4-fold less effective than that of the wild-type rt-PA. In a rabbit jugular vein clot lysis model, doses of 1.0 and 0.15 mg/kg were required for about 70% lysis in the wild-type and 37–42 variant, respectively. Fibrinogen was degraded only when the wild-type rt-PA was administered at a dose of 1.0 mg/kg. These findings suggest that the 37–42 variant can be employed at a lower dosage and that it is a more fibrin-specific thrombolytic agent than the wild-type rt-PA.

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