• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

32个分枝杆菌噬菌体基因组的同义密码子使用分析

Synonymous codon usage analysis of thirty two mycobacteriophage genomes.

作者信息

Hassan Sameer, Mahalingam Vasantha, Kumar Vanaja

机构信息

Tuberculosis Research Centre Indian Council of Medical Research, Chennai 600 031, India.

出版信息

Adv Bioinformatics. 2009;2009:316936. doi: 10.1155/2009/316936. Epub 2010 Feb 1.

DOI:10.1155/2009/316936
PMID:20150956
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2817497/
Abstract

Synonymous codon usage of protein coding genes of thirty two completely sequenced mycobacteriophage genomes was studied using multivariate statistical analysis. One of the major factors influencing codon usage is identified to be compositional bias. Codons ending with either C or G are preferred in highly expressed genes among which C ending codons are highly preferred over G ending codons. A strong negative correlation between effective number of codons (Nc) and GC3s content was also observed, showing that the codon usage was effected by gene nucleotide composition. Translational selection is also identified to play a role in shaping the codon usage operative at the level of translational accuracy. High level of heterogeneity is seen among and between the genomes. Length of genes is also identified to influence the codon usage in 11 out of 32 phage genomes. Mycobacteriophage Cooper is identified to be the highly biased genome with better translation efficiency comparing well with the host specific tRNA genes.

摘要

运用多变量统计分析方法，对32个完全测序的分枝杆菌噬菌体基因组中蛋白质编码基因的同义密码子使用情况进行了研究。确定影响密码子使用的主要因素之一是组成性偏差。在高表达基因中，以C或G结尾的密码子更受青睐，其中以C结尾的密码子比以G结尾的密码子更受高度偏爱。还观察到密码子有效数量（Nc）与GC3s含量之间存在强烈的负相关，表明密码子使用受基因核苷酸组成的影响。翻译选择也被确定在塑造翻译准确性水平上起作用的密码子使用方面发挥作用。基因组之间和内部存在高度的异质性。还确定基因长度会影响32个噬菌体基因组中11个基因组的密码子使用。分枝杆菌噬菌体库珀被确定为具有高度偏差的基因组，与宿主特异性tRNA基因相比，其翻译效率更高。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20c4/2817497/f457c5d4ca6f/ABI2009-316936.005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20c4/2817497/02c942955b82/ABI2009-316936.001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20c4/2817497/a73fb3439c67/ABI2009-316936.002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20c4/2817497/dd715a75d64f/ABI2009-316936.003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20c4/2817497/e09a9d00b266/ABI2009-316936.004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20c4/2817497/f457c5d4ca6f/ABI2009-316936.005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20c4/2817497/02c942955b82/ABI2009-316936.001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20c4/2817497/a73fb3439c67/ABI2009-316936.002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20c4/2817497/dd715a75d64f/ABI2009-316936.003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20c4/2817497/e09a9d00b266/ABI2009-316936.004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20c4/2817497/f457c5d4ca6f/ABI2009-316936.005.jpg

相似文献

1
Synonymous codon usage analysis of thirty two mycobacteriophage genomes.32个分枝杆菌噬菌体基因组的同义密码子使用分析
Adv Bioinformatics. 2009;2009:316936. doi: 10.1155/2009/316936. Epub 2010 Feb 1.
2
Synonymous codon usage in Thermosynechococcus elongatus (cyanobacteria) identifies the factors shaping codon usage variation.嗜热栖热放线菌（蓝细菌）中的同义密码子使用情况确定了影响密码子使用变异的因素。
Bioinformation. 2012;8(13):622-8. doi: 10.6026/97320630008622. Epub 2012 Jul 6.
3
Codon Usage Optimization in the Prokaryotic Tree of Life: How Synonymous Codons Are Differentially Selected in Sequence Domains with Different Expression Levels and Degrees of Conservation.原核生物树中的密码子使用优化：具有不同表达水平和不同保守程度的序列结构域中如何差异选择同义密码子。
mBio. 2020 Jul 21;11(4):e00766-20. doi: 10.1128/mBio.00766-20.
4
[Analysis of factors shaping S. pneumoniae codon usage].[影响肺炎链球菌密码子使用的因素分析]
Yi Chuan Xue Bao. 2002;29(8):747-52.
5
Looking into the genome of Thermosynechococcus elongatus (thermophilic cyanobacteria) with codon selection and usage perspective.从密码子选择和使用的角度研究嗜热蓝藻长链嗜热栖热菌的基因组。
Int J Bioinform Res Appl. 2015;11(2):130-41. doi: 10.1504/IJBRA.2015.068088.
6
Synonymous codon usage in Lactococcus lactis: mutational bias versus translational selection.乳酸乳球菌中的同义密码子使用：突变偏向与翻译选择
J Biomol Struct Dyn. 2004 Feb;21(4):527-36. doi: 10.1080/07391102.2004.10506946.
7
Synonymous codon usage in Zea mays L. nuclear genes is varied by levels of C and G-ending codons.玉米（Zea mays L.）核基因中的同义密码子使用情况因以C和G结尾的密码子水平而异。
Nucleic Acids Res. 1993 Nov 25;21(23):5294-300. doi: 10.1093/nar/21.23.5294.
8
Comparative analysis of the base composition and codon usages in fourteen mycobacteriophage genomes.十四种分枝杆菌噬菌体基因组的碱基组成和密码子使用情况的比较分析。
J Biomol Struct Dyn. 2005 Aug;23(1):63-71. doi: 10.1080/07391102.2005.10507047.
9
Preference of A/T ending codons in mitochondrial ATP6 gene under phylum Platyhelminthes: Codon usage of ATP6 gene in Platyhelminthes.扁形动物门线粒体ATP6基因中A/T结尾密码子的偏好性：扁形动物中ATP6基因的密码子使用情况
Mol Biochem Parasitol. 2018 Oct;225:15-26. doi: 10.1016/j.molbiopara.2018.08.007. Epub 2018 Aug 24.
10
Genome-wide codon usage bias analysis in Beauveria bassiana.球孢白僵菌全基因组密码子使用偏好性分析
Bioinformation. 2018 Dec 28;14(9):580-586. doi: 10.6026/97320630014580. eCollection 2018.

引用本文的文献

1
Evolution of codon usage in genomes and its impact on the host.基因组中密码子使用的演变及其对宿主的影响。
Front Vet Sci. 2023 Jan 11;9:1021440. doi: 10.3389/fvets.2022.1021440. eCollection 2022.
2
Synonymous Codon Variant Analysis for Autophagic Genes Dysregulated in Neurodegeneration.神经退行性变中自噬基因失调的同义密码子变体分析
Mol Neurobiol. 2023 Apr;60(4):2252-2267. doi: 10.1007/s12035-022-03081-1. Epub 2023 Jan 13.
3
Analysis of codon usage bias of lumpy skin disease virus causing livestock infection.引起家畜感染的结节性皮肤病病毒密码子使用偏好性分析。

本文引用的文献

1
Compositional correlation and codon usage studies in Buchnera aphidicola.蚜虫内共生菌（Buchnera aphidicola）的组成相关性和密码子使用研究。
Indian J Biochem Biophys. 2002 Feb;39(1):35-48.
2
Evaluation of codon bias perspectives in phage therapy of Mycobacterium tuberculosis by multivariate analysis.通过多变量分析评估结核分枝杆菌噬菌体治疗中的密码子偏好性观点
In Silico Biol. 2007;7(4-5):423-31.
3
Synonymous codon usage bias in 16 Staphylococcus aureus phages: implication in phage therapy.16种金黄色葡萄球菌噬菌体的同义密码子使用偏好：对噬菌体疗法的启示
Front Vet Sci. 2022 Dec 5;9:1071097. doi: 10.3389/fvets.2022.1071097. eCollection 2022.
4
An investigation of codon usage pattern analysis in pancreatitis associated genes.对胰腺炎相关基因密码子使用模式分析的研究。
BMC Genom Data. 2022 Nov 25;23(1):81. doi: 10.1186/s12863-022-01089-z.
5
Plastome structure of 8 Calanthe s.l. species (Orchidaceae): comparative genomics, phylogenetic analysis.8 种 Calanthe s.l. 物种（兰科）的质体基因组结构：比较基因组学、系统发育分析。
BMC Plant Biol. 2022 Aug 3;22(1):387. doi: 10.1186/s12870-022-03736-0.
6
Codon Usage of Hepatitis E Viruses: A Comprehensive Analysis.戊型肝炎病毒的密码子使用情况：全面分析
Front Microbiol. 2022 Jun 21;13:938651. doi: 10.3389/fmicb.2022.938651. eCollection 2022.
7
Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages.聚类 K 分枝杆菌噬菌体之间的系统发育关系和密码子使用偏性。
G3 (Bethesda). 2021 Oct 19;11(11). doi: 10.1093/g3journal/jkab291.
8
Analysis of codon usage patterns in citrus based on coding sequence data.基于编码序列数据的柑橘密码子使用模式分析。
BMC Genomics. 2020 Dec 16;21(Suppl 5):234. doi: 10.1186/s12864-020-6641-x.
9
Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes.利用组合密码子使用和分子系统发育方法对土壤细菌进行比较基因组分析，重点关注关键管家基因。
Front Microbiol. 2019 Dec 17;10:2896. doi: 10.3389/fmicb.2019.02896. eCollection 2019.
10
Codon Usage Differences among Genes Expressed in Different Tissues of Drosophila melanogaster.果蝇不同组织表达基因的密码子使用差异。
Genome Biol Evol. 2019 Apr 1;11(4):1054-1065. doi: 10.1093/gbe/evz051.
Virus Res. 2005 Nov;113(2):123-31. doi: 10.1016/j.virusres.2005.05.001.
4
Comparative analysis of the base composition and codon usages in fourteen mycobacteriophage genomes.十四种分枝杆菌噬菌体基因组的碱基组成和密码子使用情况的比较分析。
J Biomol Struct Dyn. 2005 Aug;23(1):63-71. doi: 10.1080/07391102.2005.10507047.
5
Analysis of synonymous codon usage bias in Chlamydia.衣原体同义密码子使用偏好性分析
Acta Biochim Biophys Sin (Shanghai). 2005 Jan;37(1):1-10. doi: 10.1093/abbs/37.1.1.
6
Correspondence analysis of amino acid usage within the family Bacillaceae.芽孢杆菌科内氨基酸使用情况的对应分析。
Biochem Biophys Res Commun. 2004 Dec 24;325(4):1252-7. doi: 10.1016/j.bbrc.2004.10.170.
7
Investigation on the causes of codon and amino acid usages variation between thermophilic Aquifex aeolicus and mesophilic Bacillus subtilis.嗜热栖热菌与嗜温枯草芽孢杆菌之间密码子和氨基酸使用差异原因的研究。
J Biomol Struct Dyn. 2004 Oct;22(2):205-14. doi: 10.1080/07391102.2004.10506996.
8
Evolutionary forces in shaping the codon and amino acid usages in Blochmannia floridanus.塑造佛罗里达布洛赫曼氏菌密码子和氨基酸使用情况的进化力量。
J Biomol Struct Dyn. 2004 Aug;22(1):13-23. doi: 10.1080/07391102.2004.10506976.
9
Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales.严重急性呼吸综合征冠状病毒及尼多病毒目其他病毒的同义密码子使用情况分析。
Virus Res. 2004 May;101(2):155-61. doi: 10.1016/j.virusres.2004.01.006.
10
Synonymous codon usage in Lactococcus lactis: mutational bias versus translational selection.乳酸乳球菌中的同义密码子使用：突变偏向与翻译选择
J Biomol Struct Dyn. 2004 Feb;21(4):527-36. doi: 10.1080/07391102.2004.10506946.