Base composition is the primary factor responsible for the variation of amino acid usage in zebra finch (Taeniopygia guttata).
In the present study, we carried out an examination of the amino acid usage in the zebra finch (Taeniopygia guttata) proteome. We found that tRNA abundance, base composition, hydrophobicity and aromaticity, protein second structure, cysteine residue (Cys) content and protein molecular weight had sig...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2018-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0204796 |
| _version_ | 1818725607199997952 |
|---|---|
| author | Yousheng Rao Zhangfeng Wang Wen Luo Wentao Sheng Rendian Zhang Xuewen Chai |
| author_facet | Yousheng Rao Zhangfeng Wang Wen Luo Wentao Sheng Rendian Zhang Xuewen Chai |
| author_sort | Yousheng Rao |
| collection | DOAJ |
| description | In the present study, we carried out an examination of the amino acid usage in the zebra finch (Taeniopygia guttata) proteome. We found that tRNA abundance, base composition, hydrophobicity and aromaticity, protein second structure, cysteine residue (Cys) content and protein molecular weight had significant impact on the amino acid usage of the zebra finch. The above factors explained the total variability of 22.85%, 25.37%, 10.91%, 5.06%, 4.21%, and 3.14%, respectively. Altogether, approximately 70% of the total variability in zebra finch could be explained by such factors. Comparison of the amino acid usage between zebra finch, chicken (Gallus gallus) and human (Homo sapiens) suggested that the average frequency of various amino acid usage is generally consistent among them. Correspondence analysis indicated that base composition was the primary factor affecting the amino acid usage in zebra finch. This trend was different from chicken, but similar to human. Other factors affecting the amino acid usage in zebra finch, such as isochore structure, protein second structure, Cys frequency and protein molecular weight also showed the similar trends with human. We do not know whether the similar amino acid usage trend between human and zebra finch is related to the distinctive neural and behavioral traits, but it is worth studying in depth. |
| first_indexed | 2024-12-17T21:45:00Z |
| format | Article |
| id | doaj.art-7fa55468b5db44208ef38fdd9307384e |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-17T21:45:00Z |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-7fa55468b5db44208ef38fdd9307384e2022-12-21T21:31:30ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-011312e020479610.1371/journal.pone.0204796Base composition is the primary factor responsible for the variation of amino acid usage in zebra finch (Taeniopygia guttata).Yousheng RaoZhangfeng WangWen LuoWentao ShengRendian ZhangXuewen ChaiIn the present study, we carried out an examination of the amino acid usage in the zebra finch (Taeniopygia guttata) proteome. We found that tRNA abundance, base composition, hydrophobicity and aromaticity, protein second structure, cysteine residue (Cys) content and protein molecular weight had significant impact on the amino acid usage of the zebra finch. The above factors explained the total variability of 22.85%, 25.37%, 10.91%, 5.06%, 4.21%, and 3.14%, respectively. Altogether, approximately 70% of the total variability in zebra finch could be explained by such factors. Comparison of the amino acid usage between zebra finch, chicken (Gallus gallus) and human (Homo sapiens) suggested that the average frequency of various amino acid usage is generally consistent among them. Correspondence analysis indicated that base composition was the primary factor affecting the amino acid usage in zebra finch. This trend was different from chicken, but similar to human. Other factors affecting the amino acid usage in zebra finch, such as isochore structure, protein second structure, Cys frequency and protein molecular weight also showed the similar trends with human. We do not know whether the similar amino acid usage trend between human and zebra finch is related to the distinctive neural and behavioral traits, but it is worth studying in depth.https://doi.org/10.1371/journal.pone.0204796 |
| spellingShingle | Yousheng Rao Zhangfeng Wang Wen Luo Wentao Sheng Rendian Zhang Xuewen Chai Base composition is the primary factor responsible for the variation of amino acid usage in zebra finch (Taeniopygia guttata). PLoS ONE |
| title | Base composition is the primary factor responsible for the variation of amino acid usage in zebra finch (Taeniopygia guttata). |
| title_full | Base composition is the primary factor responsible for the variation of amino acid usage in zebra finch (Taeniopygia guttata). |
| title_fullStr | Base composition is the primary factor responsible for the variation of amino acid usage in zebra finch (Taeniopygia guttata). |
| title_full_unstemmed | Base composition is the primary factor responsible for the variation of amino acid usage in zebra finch (Taeniopygia guttata). |
| title_short | Base composition is the primary factor responsible for the variation of amino acid usage in zebra finch (Taeniopygia guttata). |
| title_sort | base composition is the primary factor responsible for the variation of amino acid usage in zebra finch taeniopygia guttata |
| url | https://doi.org/10.1371/journal.pone.0204796 |
| work_keys_str_mv | AT youshengrao basecompositionistheprimaryfactorresponsibleforthevariationofaminoacidusageinzebrafinchtaeniopygiaguttata AT zhangfengwang basecompositionistheprimaryfactorresponsibleforthevariationofaminoacidusageinzebrafinchtaeniopygiaguttata AT wenluo basecompositionistheprimaryfactorresponsibleforthevariationofaminoacidusageinzebrafinchtaeniopygiaguttata AT wentaosheng basecompositionistheprimaryfactorresponsibleforthevariationofaminoacidusageinzebrafinchtaeniopygiaguttata AT rendianzhang basecompositionistheprimaryfactorresponsibleforthevariationofaminoacidusageinzebrafinchtaeniopygiaguttata AT xuewenchai basecompositionistheprimaryfactorresponsibleforthevariationofaminoacidusageinzebrafinchtaeniopygiaguttata |