酵母中的密码子使用情况：聚类分析能清晰区分高表达基因和低表达基因。
Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes.
作者信息
Sharp P M, Tuohy T M, Mosurski K R
出版信息
Nucleic Acids Res. 1986 Jul 11;14(13):5125-43. doi: 10.1093/nar/14.13.5125.
Abstract
Codon usage data has been compiled for 110 yeast genes. Cluster analysis on relative synonymous codon usage revealed two distinct groups of genes. One group corresponds to highly expressed genes, and has much more extreme synonymous codon preference. The pattern of codon usage observed is consistent with that expected if a need to match abundant tRNAs, and intermediacy of tRNA-mRNA interaction energies are important selective constraints. Thus codon usage in the highly expressed group shows a higher correlation with tRNA abundance, a greater degree of third base pyrimidine bias, and a lesser tendency to the A+T richness which is characteristic of the yeast genome. The cluster analysis can be used to predict the likely level of gene expression of any gene, and identifies the pattern of codon usage likely to yield optimal gene expression in yeast.
摘要
已收集了110个酵母基因的密码子使用数据。对相对同义密码子使用情况的聚类分析揭示了两组不同的基因。一组对应于高表达基因，并且具有更为极端的同义密码子偏好。所观察到的密码子使用模式与以下预期一致：如果需要匹配丰富的tRNA，并且tRNA-mRNA相互作用能量的中间性是重要的选择限制因素。因此，高表达组中的密码子使用与tRNA丰度具有更高的相关性，具有更大程度的第三位碱基嘧啶偏向性，并且向酵母基因组特有的A+T丰富度的倾向较小。聚类分析可用于预测任何基因的可能基因表达水平，并识别可能在酵母中产生最佳基因表达的密码子使用模式。
相似文献
1
Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes.酵母中的密码子使用情况：聚类分析能清晰区分高表达基因和低表达基因。
Nucleic Acids Res. 1986 Jul 11;14(13):5125-43. doi: 10.1093/nar/14.13.5125.
2
Coevolution of codon usage and transfer RNA abundance.密码子使用与转运RNA丰度的共同进化
Nature. 1987;325(6106):728-30. doi: 10.1038/325728a0.
3
Codon usage bias is correlated with gene expression levels in the fission yeast Schizosaccharomyces pombe.密码子使用偏好与裂殖酵母粟酒裂殖酵母中的基因表达水平相关。
Genes Cells. 2009 Apr;14(4):499-509. doi: 10.1111/j.1365-2443.2009.01284.x.
4
An evolutionary perspective on synonymous codon usage in unicellular organisms.单细胞生物同义密码子使用的进化视角
J Mol Evol. 1986;24(1-2):28-38. doi: 10.1007/BF02099948.
5
Reinvestigating the codon and amino acid usage of S. cerevisiae genome: a new insight from protein secondary structure analysis.重新研究酿酒酵母基因组的密码子和氨基酸使用情况：来自蛋白质二级结构分析的新见解。
Biochem Biophys Res Commun. 2007 Mar 16;354(3):693-9. doi: 10.1016/j.bbrc.2007.01.038. Epub 2007 Jan 17.
6
Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis.18种单细胞生物的密码子使用和tRNA基因研究以及枯草芽孢杆菌tRNA的定量分析：基于多变量分析的基因表达水平和密码子使用的物种特异性多样性
Gene. 1999 Sep 30;238(1):143-55. doi: 10.1016/s0378-1119(99)00225-5.
7
Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons.大肠杆菌调控基因中的密码子使用情况并不反映对“稀有”密码子的选择。
Nucleic Acids Res. 1986 Oct 10;14(19):7737-49. doi: 10.1093/nar/14.19.7737.
8
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.密码子适应指数——一种定向同义密码子使用偏好性的度量方法及其潜在应用。
Nucleic Acids Res. 1987 Feb 11;15(3):1281-95. doi: 10.1093/nar/15.3.1281.
9
Analyzing gene expression from relative codon usage bias in Yeast genome: a statistical significance and biological relevance.基于酵母基因组相对密码子使用偏好性分析基因表达：统计显著性与生物学相关性
Gene. 2009 Aug 15;443(1-2):121-31. doi: 10.1016/j.gene.2009.04.022. Epub 2009 May 3.
10
Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics.大肠杆菌、结核分枝杆菌和酿酒酵母中核糖体蛋白编码基因的保守密码子组成：功能基因组学中监督机器学习的经验教训
Nucleic Acids Res. 2002 Jun 1;30(11):2599-607. doi: 10.1093/nar/30.11.2599.
引用本文的文献
1
Phylogenetic Reassessment of Murinae Inferred from the Mitogenome of the Monotypic Genus Endemic to Southeast Asia: New Insights into Genetic Diversity Erosion.基于东南亚特有单型属线粒体基因组对鼠亚科系统发育的重新评估：对遗传多样性侵蚀的新见解
Biology (Basel). 2025 Jul 28;14(8):948. doi: 10.3390/biology14080948.
2
Comparative plastome analysis reveals evolutionary dynamics and codon usage patterns in Bidens (Asteraceae).比较质体基因组分析揭示了鬼针草属（菊科）的进化动态和密码子使用模式。
Funct Integr Genomics. 2025 Aug 27;25(1):175. doi: 10.1007/s10142-025-01699-7.
3
The evolution, variation, and expression patterns under development and stress responses of the NAC gene family in the barley pan-genome.大麦泛基因组中NAC基因家族在发育和胁迫响应下的进化、变异及表达模式
Front Plant Sci. 2025 Aug 7;16:1635416. doi: 10.3389/fpls.2025.1635416. eCollection 2025.
4
Genetic and codon usage analyses reveal the evolution of the seoul virus.遗传和密码子使用分析揭示了汉城病毒的进化。
Front Genet. 2025 Jun 12;16:1544577. doi: 10.3389/fgene.2025.1544577. eCollection 2025.
5
Uncovering codon usage patterns during murine embryogenesis and tissue-specific developmental diseases.揭示小鼠胚胎发育和组织特异性发育疾病过程中的密码子使用模式。
Front Genet. 2025 May 26;16:1554773. doi: 10.3389/fgene.2025.1554773. eCollection 2025.
6
A generative language model decodes contextual constraints on codon choice for mRNA design.一种生成式语言模型解码了mRNA设计中密码子选择的上下文限制。
bioRxiv. 2025 Jun 6:2025.05.13.653614. doi: 10.1101/2025.05.13.653614.
7
RSCUcaller: an R package for analyzing differences in relative synonymous codon usage (RSCU).RSCUcaller：一个用于分析相对同义密码子使用情况（RSCU）差异的R软件包。
BMC Bioinformatics. 2025 May 29;26(1):141. doi: 10.1186/s12859-025-06166-5.
8
Comparative Genomic and Phylogenetic Analysis of Chloroplasts in Mac.cv. Cocktail.Mac.cv. 鸡尾酒品种叶绿体的比较基因组学与系统发育分析
Genes (Basel). 2025 Apr 30;16(5):544. doi: 10.3390/genes16050544.
9
Mitochondrial PCGs Provide Novel Insights into Subspecies Classification, Codon Usage and Selection of Distributed in Qinghai and Gansu, China.线粒体编码基因对中国青海和甘肃分布的（物种）亚种分类、密码子使用及选择研究提供了新见解。
Animals (Basel). 2025 May 20;15(10):1486. doi: 10.3390/ani15101486.
10
Analyzing the Evolution and Host Adaptation of the Rabies Virus from the Perspective of Codon Usage Bias.从密码子使用偏好角度分析狂犬病病毒的进化与宿主适应性
Transbound Emerg Dis. 2023 Oct 10;2023:4667253. doi: 10.1155/2023/4667253. eCollection 2023.
本文引用的文献
1
Pseudogenes as a paradigm of neutral evolution.假基因作为中性进化的范例。
Nature. 1981 Jul 16;292(5820):237-9. doi: 10.1038/292237a0.
2
Codon catalog usage is a genome strategy modulated for gene expressivity.密码子编目使用是一种为基因表达性而调节的基因组策略。
Nucleic Acids Res. 1981 Jan 10;9(1):r43-74. doi: 10.1093/nar/9.1.213-b.
3
The nucleotide sequence of the HIS4 region of yeast.酵母HIS4区域的核苷酸序列。
Gene. 1982 Apr;18(1):47-59. doi: 10.1016/0378-1119(82)90055-5.
4
Nucleotide sequence comparisons and functional analysis of yeast centromere DNAs.酵母着丝粒DNA的核苷酸序列比较与功能分析。
Cell. 1982 May;29(1):235-44. doi: 10.1016/0092-8674(82)90108-8.
5
The two yeast histone H2A genes encode similar protein subtypes.这两个酵母组蛋白H2A基因编码相似的蛋白质亚型。
Proc Natl Acad Sci U S A. 1982 Mar;79(5):1484-7. doi: 10.1073/pnas.79.5.1484.
6
Codon selection in yeast.酵母中的密码子选择
J Biol Chem. 1982 Mar 25;257(6):3026-31.
7
The sequence of the DNAs coding for the mating-type loci of Saccharomyces cerevisiae.酿酒酵母交配型基因座的编码DNA序列。
Cell. 1981 Nov;27(1 Pt 2):15-23. doi: 10.1016/0092-8674(81)90356-1.
8
Histone H2B genes of yeast encode two different proteins.酵母的组蛋白H2B基因编码两种不同的蛋白质。
Cell. 1980 Dec;22(3):799-805. doi: 10.1016/0092-8674(80)90556-5.
9
Structure of a split yeast gene: complete nucleotide sequence of the actin gene in Saccharomyces cerevisiae.一个分裂酵母基因的结构：酿酒酵母肌动蛋白基因的完整核苷酸序列。
Proc Natl Acad Sci U S A. 1980 May;77(5):2546-50. doi: 10.1073/pnas.77.5.2546.
10
Codon catalog usage and the genome hypothesis.密码子目录使用与基因组假说。
Nucleic Acids Res. 1980 Jan 11;8(1):r49-r62. doi: 10.1093/nar/8.1.197-c.
Zotero 插件