Non-uniqueness of factors constraint on the codon usage in Bombyx mori.
Non-uniqueness of factors constraint on the codon usage in Bombyx mori.
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家蚕密码子使用限制因素的非唯一性
DOI：
10.1186/s12864-015-1596-z
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发表时间：
2015-05-06
期刊：
影响因子：
4.4
通讯作者：
Sun J
中科院分区：
文献类型：
--
作者：
Jia X;Liu S;Zheng H;Li B;Qi Q;Wei L;Zhao T;He J;Sun J
研究背景对密码子使用的分析是了解生物体遗传和进化特征的好方法。然而，关于家蚕(Bombyx mori(B.mori))密码子使用的报道却很少。因此，本文对家蚕B.mori的密码子使用情况进行了分析，以揭示制约因素，为改进基于B.mori的生物反应器提供帮助。结果共分析了1,097条注释的家蚕mRNA序列，发现只有微弱的密码子偏好。基因表达水平与GC含量以及总平均亲水性(肉汁)和芳香性(Aromo)较高的氨基酸有关。主轴上的基因与GC含量、GC3s呈极显著正相关。同时，密码子的有效数目(ENC)与密码子适应指数(CAI)、基因长度和ARMO值密切相关。然而，ENC值与第二轴相关，这表明家蚕密码子的使用不仅受到突变压力和自然选择的影响，还受到核苷酸组成和基因表达水平的影响。它还与Aromo值和基因长度有关。此外，家蚕与黑腹果蝇和酿酒酵母的密码子偏好有较大差异，而与拟南芥、大肠杆菌和线虫的密码子偏好差异较大。结论家蚕对密码子的偏好性较弱，存在核苷酸组成、突变压力、自然选择和表达水平等多种影响因素。此外，它还与Aromo值和基因长度有关。其中，自然选择可能发挥重要作用。此外，家蚕最佳密码子均由G和C编码，这为通过密码子优化提高家蚕基因表达水平提供了有用的信息。
BackgroundThe analysis of codon usage is a good way to understand the genetic and evolutionary characteristics of an organism. However, there are only a few reports related with the codon usage of the domesticated silkworm, Bombyx mori (B. mori). Hence, the codon usage of B. mori was analyzed here to reveal the constraint factors and it could be helpful to improve the bioreactor based on B. mori.ResultsA total of 1,097 annotated mRNA sequences from B. mori were analyzed, revealing there is only a weak codon bias. It also shows that the gene expression level is related to the GC content, and the amino acids with higher general average hydropathicity (GRAVY) and aromaticity (Aromo). And the genes on the primary axis are strongly positively correlated with the GC content, and GC3s. Meanwhile, the effective number of codons (ENc) is strongly correlated with codon adaptation index (CAI), gene length, and Aromo values. However, the ENc values are correlated with the second axis, which indicates that the codon usage in B. mori is affected by not only mutation pressure and natural selection, but also nucleotide composition and the gene expression level. It is also associated with Aromo values, and gene length. Additionally, B. mori has a greater relative discrepancy in codon preferences with Drosophila melanogaster (D. melanogaster) or Saccharomyces cerevisiae (S. cerevisiae) than with Arabidopsis thaliana (A. thaliana), Escherichia coli (E. coli), or Caenorhabditis elegans (C. elegans).ConclusionsThe codon usage bias in B. mori is relatively weak, and many influence factors are found here, such as nucleotide composition, mutation pressure, natural selection, and expression level. Additionally, it is also associated with Aromo values, and gene length. Among them, natural selection might play a major role. Moreover, the “optimal codons” of B. mori are all encoded by G and C, which provides useful information for enhancing the gene expression in B. mori through codon optimization.
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DOI：
10.1073/pnas.96.8.4482
发表时间：
1999-04-13
影响因子：
11.1
作者：
Duret, L;Mouchiroud, D
通讯作者：
Mouchiroud, D
影响因子：
2.4
作者：
Peixoto, L;Fernández, V;Musto, H
通讯作者：
Musto, H
影响因子：
3.9
作者：
LI, WH
通讯作者：
LI, WH
DOI：
10.1073/pnas.85.8.2653
发表时间：
1988-04-01
影响因子：
11.1
作者：
SUEOKA, N
通讯作者：
SUEOKA, N
DOI：
10.1016/j.bbrc.2014.06.087
发表时间：
2014-07-25
影响因子：
3.1
作者：
Ihara, Hideyuki;Okada, Takahiro;Ikeda, Yoshitaka
通讯作者：
Ikeda, Yoshitaka