一个进化视角的Codon使用模式,dinucleotide组成和Codon对偏差在普鲁努斯死环斑病毒中
Lingqi Wang1,2, Haiting Zhao2, Zhilei Wang2
1College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China.
Genes
|September 28, 2023
概括
普鲁努斯死环斑病毒 (PNRSV) 的进化是由自然选择驱动的,而不仅仅是突变. 对其外套蛋白质基因的分析揭示了特定的二核酸偏好和低密码对偏差,为病毒遗传多样性提供了洞察力.
科学领域:
- * 病毒学 病毒学
- * 进化生物学 进化生物学
- * 生物信息学是一门学科.
背景情况:
- * 普鲁努斯死环斑病毒 (PNRSV) 严重影响园艺产业.
- *以前的研究集中在PNRSV多样性和检测上,使得代码使用偏差 (CUB),二核酸偏好和代码对偏差 (CPB) 不确定.
- *了解这些遗传特征对于理解PNRSV演变和管理至关重要.
研究的目的:
- *全面分析PNRSV外套蛋白 (CP) 基因的CUB,二核酸组成和CPB.
- * 调查PNRSV遗传特征背后的驱动力,包括自然选择和突变.
- * 探索二核酸组成与病毒因素 (如血统,宿主和代码子位置) 之间的关系.
主要方法:
- *分析了359个PNRSV CP基因序列.
- * 检查子使用偏差 (CUB).
- *对二核酸组合和子对偏差 (CPB) 的评估.
主要成果:
- *对于PNRSV CUB来说,自然选择是一个比突变更重要的驱动力.
- *观察到CpC/GpA的过度表达和UpA/GpC二核酸的表达不足.
- * 双核酸组成与病毒密码子位置有很强的关联,但与血统和宿主有很弱的联系.
- *PNRSV CP基因表现出较低的CPB,受二核酸偏好和密码体使用模式的影响.
结论:
- *自然选择在塑造PNRSV编码子使用方面发挥着主导作用.
- * 特定的二核酸偏好和低的CPB是PNRSV CP基因的特征.
- *研究结果为未来研究PNRSV遗传多样性和进化机制提供了基础.
相关概念视频
Bacterial RNA Polymerase
29.6K
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
29.6K
Viral Mutations
32.4K
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
32.4K
Cis-regulatory Sequences
9.9K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
9.9K
Size and Structure of Viral Genomes
51
Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
51
Bacterial Transcription
28.4K
RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
28.4K
Leaky Scanning
5.2K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.2K


