Related Experiment Video
Updated: May 13, 2026
07:55
Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
Published on: May 31, 2011
Structural basis of core promoter recognition in a primitive eukaryote
Maria A Schumacher1, Audrey O T Lau, Patricia J Johnson
1Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA. schumacm@ohsu.edu
Cell
|November 19, 2003
Summary
Trichomonas vaginalis uses initiator binding protein 39 kDa (IBP39) to select transcription start sites. IBP39 directly recruits RNA Polymerase II (RNAP II) via its C-terminal domain, initiating transcription.
Area of Science:
- Molecular Biology
- Eukaryotic Transcription
- Structural Biology
Background:
- Transcription start site (TSS) selection in eukaryotes relies on promoter elements like TATA, initiator (Inr), and downstream promoter element (DPE).
- Trichomonas vaginalis, an ancient eukaryote, uniquely utilizes the Inr for TSS selection, recognized by initiator binding protein 39 kDa (IBP39).
Purpose of the Study:
- To elucidate the structural basis of Inr recognition and RNAP II recruitment by IBP39 in T. vaginalis.
- To understand the mechanism of transcription initiation in this ancient eukaryote.
Main Methods:
- X-ray crystallography to determine the structures of IBP39 domains (IBD and C domain) and their complexes.
- Biochemical assays to investigate interactions between IBP39 and T. vaginalis RNAP II.
Main Results:
- Crystal structures revealed the winged-helix motif of the IBD, sharing features with prokaryotic and eukaryotic proteins.
- The C domain of IBP39 was shown to interact with the C-terminal domain of T. vaginalis RNAP II.
- IBP39 binds the Inr via its IBD, facilitating direct recruitment of RNAP II.
Conclusions:
- IBP39 acts as a direct bridge between the Inr and RNAP II in T. vaginalis.
- This mechanism highlights a potentially ancestral pathway for transcription initiation in eukaryotes.
Related Concept Videos
01:58Prokaryotic Transcriptional Activators and Repressors
The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.
Transcription of prokaryotic...
Transcription of prokaryotic...
02:40The Eukaryotic Promoter Region
The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
02:42Eukaryotic Transcription Activators
Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
The binding domains are capable of recognizing and interacting with regulatory sequences on the DNA. These domains are...
The binding domains are capable of recognizing and interacting with regulatory sequences on the DNA. These domains are...
01:58Prokaryotic Transcriptional Activators and Repressors
The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.
Transcription of prokaryotic...
Transcription of prokaryotic...
02:40The Eukaryotic Promoter Region
The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
01:28Prokaryotic Gene Structure and Organization
Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...