Related Experiment Video
Updated: Jun 9, 2025
10:58
Plant Promoter Analysis: Identification and Characterization of Root Nodule Specific Promoter in the Common Bean
Published on: December 23, 2017
12.6K
BEAN and HABAS: Polyphyletic insertions in the DNA-directed RNA polymerase
Claudia Alvarez-Carreño1, Angela T Huynh2, Anton S Petrov2,3
1Institute of Structural and Molecular Biology, University College London, London, UK.
Protein Science : a Publication of the Protein Society
|October 28, 2024
Summary
New domains, BEAN and HABAS, were identified in bacterial RNA polymerase (RNAP) subunits. Their phylogenetic distribution offers insights into protein evolution and evolutionary timelines.
Area of Science:
- Molecular Biology
- Evolutionary Biology
- Structural Biology
Background:
- RNA polymerase (RNAP) subunits β and β' possess complex multi-domain structures.
- Insertional domains are key features within these large proteins.
- Understanding domain organization is crucial for deciphering protein function and evolution.
Purpose of the Study:
- To analyze the domain organization of bacterial RNAP-β and RNAP-β' subunits.
- To identify and characterize lineage-specific insertional domains.
- To investigate the evolutionary implications of these domains.
Main Methods:
- Sequence analysis
- Analysis of experimentally determined protein structures
- AlphaFold structure predictions
Main Results:
- Identified the BEAN (broadly embedded annex) domain in bacterial RNAP-β.
- Identified the HABAS (hammerhead/barrel-sandwich hybrid) domain in bacterial RNAP-β'.
- Observed homologous insertional domains in archaeal ribosomal protein L10 and various metabolic proteins.
- Demonstrated that the phylogenetic distribution of these domains aligns with the Tree of Life.
Conclusions:
- The BEAN and HABAS domains represent significant lineage-specific insertions in bacterial RNAP subunits.
- The presence and distribution of these domains provide a relative timeline for protein evolution.
- Homologous insertional domains in non-equivalent locations across bacteria and archaea suggest complex evolutionary mechanisms.
Related Concept Videos
00:43Bacterial RNA Polymerase
29.1K
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...
29.1K
00:58Eukaryotic RNA Polymerases
23.7K
RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
All three eukaryotic RNAPs require specific transcription factors, of which the...
23.7K
02:57DNA-only Transposons
14.4K
DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
The donor site from where the transposon is excised is either degraded or...
14.4K
02:57piRNA - Piwi-interacting RNAs
6.8K
PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...
6.8K
02:36RNA Polymerase II Accessory Proteins
9.1K
Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
9.1K
01:02Long-patch Base Excision Repair
7.0K
Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:
7.0K