Related Experiment Video
Updated: May 30, 2026
09:20
In situ Subcellular Fractionation of Adherent and Non-adherent Mammalian Cells
Published on: July 23, 2010
Evolutionary variation of papillomavirus E2 protein and E2 binding sites.
Adam Rogers1, Mackenzie Waltke, Peter C Angeletti
1Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA.
Virology Journal
|August 3, 2011
Summary
Papillomavirus E2 binding sites show distinct evolutionary patterns. Alpha-papillomaviruses exhibit conserved inverted linkers in E2 binding sites, suggesting functional importance in viral evolution.
Area of Science:
- Virology
- Molecular Evolution
- Bioinformatics
Background:
- Investigating evolutionary changes in papillomavirus E2 function across genera.
- Analyzing E2 binding sites (E2BS) within the long control region (LCR) and genomes.
- Examining sequence conservation and nucleotide content of E2BS spacers.
Purpose of the Study:
- To identify evolutionary changes in papillomavirus E2 function.
- To compare E2BS sequences and nucleotide content across major papillomavirus genera.
- To understand the evolutionary dynamics of the E2 protein.
Main Methods:
- Identified E2BS in 128 genomes from six papillomavirus genera (Alpha, Beta, Gamma, Delta, Lambda, Xi).
- Compared sequences to a consensus model derived from known functional E2BS.
- Performed multiple sequence alignments of E2 protein sequences and phylogenetic analysis.
Main Results:
- Significant differences in GC content of the E2BS spacer were found between Alpha and Delta papillomaviruses.
- Phylogenetic analysis of E2 amino acid sequences revealed two distinct subgroups within Alpha-papillomaviruses (α1 and α2).
- Subgroup α1 favored an AAAA spacer, while subgroup α2 favored a TTTT spacer, indicating conserved inverted linkers.
Conclusions:
- The distinct E2BS spacer sequences in Alpha-papillomavirus subgroups suggest functional divergence.
- Conserved inverted linkers within E2BS may play a role in papillomavirus evolution and E2 function.
- Evolutionary analysis of E2BS provides insights into papillomavirus diversity and host interactions.
Related Concept Videos
02:28Leaky Scanning
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 stands for...
02:33Initiation of Translation
Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
00:36Viral Mutations
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 for adaptive...
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
02:31Synteny and Evolution
John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral chromosome underwent...
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral chromosome underwent...
02:26Conservation of Protein Domains Over Different Proteins
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...