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GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes

Overview of attention for article published in BMC Genomics, May 2018
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Title
GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes
Published in
BMC Genomics, May 2018
DOI 10.1186/s12864-018-4684-z
Pubmed ID
Authors

Dongsheng Zhang, Peng Hu, Taigang Liu, Jian Wang, Shouwen Jiang, Qianghua Xu, Liangbiao Chen

Abstract

Temperature adaptation of biological molecules is fundamental in evolutionary studies but remains unsolved. Fishes living in cold water are adapted to low temperatures through adaptive modification of their biological molecules, which enables their functioning in extreme cold. To study nucleotide and amino acid preference in cold-water fishes, we investigated the substitution asymmetry of codons and amino acids in protein-coding DNA sequences between cold-water fishes and tropical fishes., The former includes two Antarctic fishes, Dissostichus mawsoni (Antarctic toothfish), Gymnodraco acuticeps (Antarctic dragonfish), and two temperate fishes, Gadus morhua (Atlantic cod) and Gasterosteus aculeatus (stickleback), and the latter includes three tropical fishes, including Danio rerio (zebrafish), Oreochromis niloticus (Nile tilapia) and Xiphophorus maculatus (Platyfish). Cold-water fishes showed preference for Guanines and cytosines (GCs) in both synonymous and nonsynonymous codon substitution when compared with tropical fishes. Amino acids coded by GC-rich codons are favored in the temperate fishes, while those coded by AT-rich codons are disfavored. Similar trends were discovered in Antarctic fishes but were statistically weaker. The preference of GC rich codons in nonsynonymous substitution tends to increase ratio of small amino acid in proteins, which was demonstrated by biased small amino acid substitutions in the cold-water species when compared with the tropical species, especially in the temperate species. Prediction and comparison of secondary structure of the proteomes showed that frequency of random coils are significantly larger in the cold-water fish proteomes than those of the tropical fishes. Our results suggested that natural selection in cold temperature might favor biased GC content in the coding DNA sequences, which lead to increased frequency of small amino acids and consequently increased random coils in the proteomes of cold-water fishes.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 33 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 33 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 7 21%
Student > Ph. D. Student 4 12%
Student > Bachelor 3 9%
Professor 2 6%
Student > Doctoral Student 2 6%
Other 6 18%
Unknown 9 27%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 10 30%
Agricultural and Biological Sciences 10 30%
Medicine and Dentistry 1 3%
Chemistry 1 3%
Materials Science 1 3%
Other 0 0%
Unknown 10 30%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 15 March 2023.
All research outputs
#14,405,826
of 23,539,593 outputs
Outputs from BMC Genomics
#5,481
of 10,789 outputs
Outputs of similar age
#180,287
of 327,560 outputs
Outputs of similar age from BMC Genomics
#117
of 243 outputs
Altmetric has tracked 23,539,593 research outputs across all sources so far. This one is in the 37th percentile – i.e., 37% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,789 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 46th percentile – i.e., 46% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 327,560 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 43rd percentile – i.e., 43% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 243 others from the same source and published within six weeks on either side of this one. This one is in the 48th percentile – i.e., 48% of its contemporaries scored the same or lower than it.