GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes
Abstract Background 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...
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ftdoajarticles:oai:doaj.org/article:ec07c7ca53c948ca91223ec2db5e8d41 2023-05-15T13:53:05+02:00 GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes Dongsheng Zhang Peng Hu Taigang Liu Jian Wang Shouwen Jiang Qianghua Xu Liangbiao Chen 2018-05-01T00:00:00Z https://doi.org/10.1186/s12864-018-4684-z https://doaj.org/article/ec07c7ca53c948ca91223ec2db5e8d41 EN eng BMC http://link.springer.com/article/10.1186/s12864-018-4684-z https://doaj.org/toc/1471-2164 doi:10.1186/s12864-018-4684-z 1471-2164 https://doaj.org/article/ec07c7ca53c948ca91223ec2db5e8d41 BMC Genomics, Vol 19, Iss 1, Pp 1-10 (2018) Cold adaptation Substitution bias Cold-water Antarctic Genome Fish Biotechnology TP248.13-248.65 Genetics QH426-470 article 2018 ftdoajarticles https://doi.org/10.1186/s12864-018-4684-z 2022-12-31T05:26:56Z Abstract Background 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). Results 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. Conclusions 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. Article in Journal/Newspaper Antarc* Antarctic Antarctic Toothfish atlantic cod Gadus morhua Directory of Open Access Journals: DOAJ Articles Antarctic BMC Genomics 19 1 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
topic |
Cold adaptation Substitution bias Cold-water Antarctic Genome Fish Biotechnology TP248.13-248.65 Genetics QH426-470 |
spellingShingle |
Cold adaptation Substitution bias Cold-water Antarctic Genome Fish Biotechnology TP248.13-248.65 Genetics QH426-470 Dongsheng Zhang Peng Hu Taigang Liu Jian Wang Shouwen Jiang Qianghua Xu Liangbiao Chen GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes |
topic_facet |
Cold adaptation Substitution bias Cold-water Antarctic Genome Fish Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
Abstract Background 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). Results 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. Conclusions 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. |
format |
Article in Journal/Newspaper |
author |
Dongsheng Zhang Peng Hu Taigang Liu Jian Wang Shouwen Jiang Qianghua Xu Liangbiao Chen |
author_facet |
Dongsheng Zhang Peng Hu Taigang Liu Jian Wang Shouwen Jiang Qianghua Xu Liangbiao Chen |
author_sort |
Dongsheng Zhang |
title |
GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes |
title_short |
GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes |
title_full |
GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes |
title_fullStr |
GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes |
title_full_unstemmed |
GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes |
title_sort |
gc bias lead to increased small amino acids and random coils of proteins in cold-water fishes |
publisher |
BMC |
publishDate |
2018 |
url |
https://doi.org/10.1186/s12864-018-4684-z https://doaj.org/article/ec07c7ca53c948ca91223ec2db5e8d41 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic Antarctic Toothfish atlantic cod Gadus morhua |
genre_facet |
Antarc* Antarctic Antarctic Toothfish atlantic cod Gadus morhua |
op_source |
BMC Genomics, Vol 19, Iss 1, Pp 1-10 (2018) |
op_relation |
http://link.springer.com/article/10.1186/s12864-018-4684-z https://doaj.org/toc/1471-2164 doi:10.1186/s12864-018-4684-z 1471-2164 https://doaj.org/article/ec07c7ca53c948ca91223ec2db5e8d41 |
op_doi |
https://doi.org/10.1186/s12864-018-4684-z |
container_title |
BMC Genomics |
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19 |
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1 |
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1766258045952720896 |