scholarly journals Nucleotide Polymorphism and Natural Selection at the Pantophysin (Pan I) Locus in the Atlantic Cod, Gadus morhua (L.)

Genetics ◽  
2001 ◽  
Vol 157 (1) ◽  
pp. 317-330 ◽  
Author(s):  
Grant H Pogson
Keyword(s):  
Natural Selection ◽  
Amino Acid ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Amino Acid Level ◽  
Amino Acid Substitutions ◽  
Significant Heterogeneity ◽  
Nucleotide Sequence Variation ◽  
Spatially Varying ◽  
Spatially Varying Selection

Abstract Molecular studies of nucleotide sequence variation have rarely attempted to test hypotheses related to geographically varying patterns of natural selection. The present study tested the role of spatially varying selection in producing significant linkage disequilibrium and large differences in the frequencies of two common alleles at the pantophysin (Pan I) locus among five populations of the Atlantic cod, Gadus morhua. Nucleotide sequences of 124 Pan I alleles showed strong evidence for an unusual mix of balancing and directional selection but no evidence of stable geographically varying selection. The alleles were highly divergent at both the nucleotide level (differing on average by 19 mutations) and at amino acid level (each having experienced three amino acid substitutions since diverging from a common ancestral allele). All six amino acid substitutions occurred in a 56-residue intravesicular loop (IV1 domain) of the vesicle protein and each involved a radical change. An analysis of molecular variation revealed significant heterogeneity in the frequencies of recently derived mutations segregating within both allelic classes, suggesting that two selective sweeps may be presently occurring among populations. The dynamic nature of the Pan I polymorphism in G. morhua and clear departure from equilibrium conditions invalidate a simple model of spatially varying selection.

Viral fitness and antigenic determinants of porcine parvovirus at the amino acid level of the capsid protein

2021 ◽  
Author(s):  
André Felipe Streck ◽  
Cláudio Wageck Canal ◽  
Uwe Truyen
Keyword(s):  
Amino Acid ◽  
Capsid Protein ◽  
Immune Escape ◽  
Amino Acid Level ◽  
Binding Activity ◽  
Viral Fitness ◽  
Antigenic Determinants ◽  
Amino Acid Substitutions ◽  
Porcine Parvovirus ◽  
Predominant Factor

Since 2001, strains of porcine parvovirus (PPV), designated 27a -like strains, were observed in Europe, suggesting a predominance of these viruses over older strains. The reasons for the obvious evolutionary advantage are unknown. Here, a series of mutants containing amino acid replacements found in the predominant field strains were generated in a PPV-NADL2 background and their impact on replication efficiency and antibody binding activity was determined. Some amino acid substitutions observed in the 27a- like strains significantly increased viral fitness and decreased neutralization activity of sera raised against commercial vaccines and old virus strains (e.g. NADL2). These mutant viruses and a monoclonal antibody raised against a classical PPV strain defined an 27a-specific neutralizing epitope around amino acid 228 of the capsid protein VP2. Based on the analysis of the mutant viruses, it is hypothesized that the predominant factor for the global spread of the PPV-27a strain substitutions is an increased viral fitness of the 27a- like viruses, possibly supported by a partial immune selection. This is reminiscent to the evolution of canine parvovirus and worldwide replacement of the original virus by the so-called new antigenic types. Importance Porcine parvovirus is one of the most important causes of reproductive failure in swine. Recently, despite the continuous use of vaccines, “new” strains emerged, leading to the hypothesis that the emergence of new amino acid substitutions could be a viral adaptation to the immune response against the commercial vaccines. Our results indicate the amino acid substitutions observed in the 27a -like strains can modify viral fitness and antigenicity. However, an absolute immune escape was not evident.

Effect of age and temperature on amino acid composition and the content of different protein types of juvenile Atlantic cod (Gadus morhua) otoliths

2004 ◽  
Vol 61 (6) ◽  
pp. 1012-1020 ◽  
Author(s):  
K Hüssy ◽  
H Mosegaard ◽  
F Jessen
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Soluble Protein ◽  
Protein Fraction ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Water Soluble ◽  
Soluble Protein Fraction ◽  
Water Soluble Protein

The purpose of this study was to analyse the amino acid composition of otolith matrix protein, estimate the proportion of the water-soluble protein fraction, and analyse the effect of matrix composition on otolith visual appearance. Juvenile Atlantic cod (Gadus morhua) were reared under constant temperature and feeding conditions and sampled at the beginning and the end of the experiment. The amino acid composition was dominated by asparagine, glutamic acid, leucine, serine, and proline. A change in amino acid composition was observed with increasing temperature and time, caused by changing proportions of the water-soluble and -insoluble protein fractions. Feeding level had no effect. The relative content of water-soluble protein was linearly related to fish dry weight and temperature. Otolith opacity, defined as the percentage of incident light absorbed by an otolith section, did not differ significantly between experimental treatments. The soluble protein fraction had a positive, albeit insignificant, correlation with opacity. Using opacity and otolith volume, deposited total otolith protein content was estimated with an R2 of 0.91, where otolith volume alone explained 83% of the observed variation.

scholarly journals Evolutionary Analyses of RNA Editing and Amino Acid Recoding in Cephalopods

2019 ◽  
Author(s):  
Mingye (Christina) Wang ◽  
Erik Mohlhenrich
Keyword(s):  
Amino Acid ◽  
Candidate Genes ◽  
Rna Editing ◽  
Amino Acid Level ◽  
Nucleotide Composition ◽  
Model Organisms ◽  
Future Research ◽  
Amino Acid Substitutions ◽  
Behavioral Complexity ◽  
Fitness Advantage

AbstractRNA editing is a post-transcriptional modification process that alters nucleotides of mRNA and consequently the amino acids of the translated protein without changing the original DNA sequence. In human and other mammals, amino acid recoding from RNA editing is rare, and most edits are non-adaptive and provide no fitness advantage (1). However, recently it was discovered that in soft-bodied cephalopods, which are exceptionally intelligent and include squid, octopus, and cuttlefish, RNA editing is widespread and positively selected (2). To examine the effects of RNA editing on individual genes, we developed a “diversity score” system that quantitatively assesses the amount of diversity generated in each gene, incorporating combinatorial diversity and the radicalness of amino acid changes. Using this metric, we compiled a list of top 100 genes across the cephalopod species that are most diversified by RNA editing. This list of candidate genes provides directions for future research into the specific functional impact of RNA editing in terms of protein structure and cellular function on individual proteins. Additionally, considering the connection of RNA editing to the nervous system, and the exceptional intelligence of cephalopod, the candidate genes may shed light to the molecular development of behavioral complexity and intelligence. To further investigate global influences of RNA editing on the transcriptome, we investigated changes in nucleotide composition and codon usage biases in edited genes and coleoid transcriptome in general. Results show that these features indeed correlate with editing and may correspond to causes or effects of RNA editing. In addition, we characterized the unusual RNA editing in cephalopods by analyzing ratio of radical to conservative amino acid substitutions (R/C) and distribution of amino acid recoding from editing. Our results show that compared to model organisms, editing in cephalopods have significantly decreased R/C ratio and distinct distribution of amino acid substitutions that favor conservative over radical changes, indicating selection at the amino acid level and providing a potential mechanism for the evolution of widespread RNA editing in cephalopods.

Antifreeze glycoproteins in the plasma of Newfoundland Atlantic cod (Gadus morhua)

1981 ◽  
Vol 59 (11) ◽  
pp. 2186-2192 ◽  
Author(s):  
Choy L. Hew ◽  
Don Slaughter ◽  
Garth L. Fletcher ◽  
Shashikant B. Joshi
Keyword(s):  
Amino Acid ◽  
High Performance ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Antifreeze Proteins ◽  
Gel Filtration ◽  
Exchange Chromatography ◽  
Polar Cod ◽  
Antifreeze Glycoproteins ◽  
Molecular Weights

The plasma of the Atlantic cod, Gadus morhua, contained antifreeze glycoproteins which were present only during the winter months. The antifreeze proteins were isolated, using gel filtration and ion exchange chromatography, and characterized by high performance liquid chromatography. The antifreeze proteins appeared to consist of at least seven components with molecular weights ranging from 2 500 to 33 000. Chemical analysis of the larger components showed a predominance of alanine, threonine, and galactosamine in a ratio of 2:1:1. The smaller peptides contained proline, in addition to alanine and threonine. The amino acid sequence of the smallest glycopeptide (molecular weight 2500) was found to be Ala Ala Thr Pro Ala Thr Ala Ala Thr Pro Ala Thr Ala Ala.These glycoproteins are very similar, if not identical, in amino acid and carbohydrate composition to those isolated from Antaractic nototheniids and several northern gadoids. The sequence of the smallest glycopeptide from the Atlantic cod is identical to that reported for the polar cod, Boreogadus saida.

Primary structure, distribution, and effects on motility of CGRP in the intestine of the cod Gadus morhua

1998 ◽  
Vol 275 (1) ◽  
pp. R19-R28 ◽  
Author(s):  
Fatemeh Shahbazi ◽  
Paul Karila ◽  
Catharina Olsson ◽  
Susanne Holmgren ◽  
J. Michael Conlon ◽  
...  
Keyword(s):  
Amino Acid ◽  
Primary Structure ◽  
Myenteric Plexus ◽  
Gadus Morhua ◽  
Circular Muscle ◽  
Muscle Layer ◽  
Inhibitory Response ◽  
Nerve Fibers ◽  
Amino Acid Substitutions ◽  
Circular Muscle Layer

Calcitonin gene-related peptide (CGRP) was isolated from an extract of the intestine of the cod Gadus morhua. The primary structure of this 37-amino acid peptide was established as follows: ACNTA TCVTH RLADF LSRSG GIGNS NFVPT NVGSK AF-NH2. The peptide shows close structural similarities to other nonmammalian (3–4 amino acid substitutions) and mammalian (5–8 amino acid substitutions) CGRPs, and it contains the two residues Asp14 and Phe15 that seem to be characteristic for CGRP in nonmammalian vertebrates. Cod CGRP (10−9–10−7M) inhibited the motility of spontaneously active ring preparations from the cod intestine and was significantly ( P < 0.05) more potent than rat α-CGRP. Neither prostaglandins nor nitric oxide is involved in the inhibitory response produced by cod CGRP, and the lack of effect of tetrodotoxin suggests an action of CGRP on receptors on the intestinal smooth muscle cells. The competitive CGRP antagonist human α-CGRP-(8—37) significantly ( P < 0.05) reduced the response to cod CGRP. Immunohistochemistry demonstrated CGRP-immunoreactive neurons intrinsic to the intestine, and a dense innervation with immunoreactive nerve fibers was observed in the myenteric plexus and the circular muscle layer. Myotomy studies show that CGRP-containing nerves project orally and anally in the myenteric plexus, whereas nerve fibers in the circular muscle layer project mainly anally, indicating a role for CGRP in descending inhibitory pathways of the cod intestine.

Effects of amino acid supplementations on metabolic and physiological parameters in Atlantic cod (Gadus morhua) under stress

2016 ◽  
Vol 43 (2) ◽  
pp. 591-602 ◽  
Author(s):  
Marcelino Herrera ◽  
María Antonia Herves ◽  
Inmaculada Giráldez ◽  
Kristin Skar ◽  
Hanne Mogren ◽  
...  
Keyword(s):  
Amino Acid ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Physiological Parameters

Amino Acid Decarboxylase Activity and Other Chemical Characteristics as Related to Freshness Loss in Iced Cod (Gadus morhua)†

2002 ◽  
Vol 65 (7) ◽  
pp. 1152-1157 ◽  
Author(s):  
M. MANUELA HERNÁNDEZ-HERRERO ◽  
GUILLAUME DUFLOS ◽  
PIERRE MALLE ◽  
STÉPHANE BOUQUELET
Keyword(s):  
Amino Acid ◽  
Biogenic Amine ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Storage Period ◽  
Acid Decarboxylase ◽  
Decarboxylase Activity ◽  
Exponential Relationship ◽  
Sensory Score ◽  
Iced Storage

Biogenic amine levels and other biochemical indicators were measured to study the safety of and the loss of freshness in iced Atlantic cod. Biogenic amine content exhibited high variability during iced storage of Atlantic cod. Ornithine and lysine decarboxylase activity apparently increased at the end of the storage period. Amino acid activity was probably generated by endogenous amino acid decarboxylases of raw fish. No statistical differences were observed in the total volatile base fraction or in the ammonia or monomethylamine contents during iced storage. However, trimethylamine contents showed a significant exponential relationship with time and sensory score. Cod formed inosine as the major metabolite of IMP. The H and G indices showed a linear relationship with time and sensory score and served as good indicators of cod freshness quality. However, the K, Ki, and P indices showed a logarithmic relationship with time and sensory score. IMP, K, Ki, and P served as indicators of freshness lost during the early stages of chilled storage of cod.

Structure and Proposed Amino-Acid Sequence of a Pepsin from Atlantic Cod (Gadus morhua)

1998 ◽  
Vol 54 (1) ◽  
pp. 32-46 ◽  
Author(s):  
Solveig Karlsen ◽  
Edward Hough ◽  
Ragnar L. Olsen
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Gadus Morhua ◽  
Model Building ◽  
Atlantic Cod ◽  
Tuna Fish ◽  
Area Detector ◽  
Replacement Method ◽  
Molecular Replacement Method ◽  
Starting Model

The crystal structure of a pepsin from the gastric mucosa of Atlantic cod has been determined to 2.16 Å resolution. Data were collected on orthorhombic crystals with cell dimensions a = 35.98, b = 75.40 and c = 108.10 Å, on a FAST area-detector system. The phase problem was solved by the molecular-replacement method using porcine pepsin (PDB entry 5PEP) as a search model. The structure has been refined to a crystallographic R factor of 20.8% using all reflections between 8.0 and 2.16 Å, without prior knowedge of the primary sequence. The resulting crystal structure is very similar to the porcine enzyme, consisting of two domains with predominantly β-sheet structure in the same sequential positions as the enzyme from pig. In the course of the model building, 122 residues were substituted and two residues deleted from the starting model to give a polypeptide chain of 324 amino acids and a sequence identity of 57.7% with the pig pepsin. No carbohydrate residues were located. Sequence alignment with available aspartic proteinases, indicates that the fish enzyme seems to be more related to mammalian gastric pepsins than to the mammalian gastricsins and chymosins, lysosomal cathepsin D's and a pepsin from tuna fish. The amino-acid composition of the cod enzyme, however, is more in accordance with the cathepsin D's.

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