Related Experiment Video
Updated: Aug 13, 2026

07:09
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
Molecular evolution of the AP2 subfamily
Mikao Shigyo1, Mitsuyasu Hasebe, Motomi Ito
1Department of General System Studies, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Tokyo 153-8902, Japan.
Gene
|January 4, 2006
Summary
The AP2 (APETALA2)/EREBP (Ethylene Responsive Element Binding Protein) gene family
Area of Science:
- Plant molecular biology
- Evolutionary genetics
- Transcriptional regulation
Background:
- The APETALA2 (AP2)/Ethylene Responsive Element Binding Protein (EREBP) multigene family encodes crucial transcription factors.
- AP2/EREBP genes are classified into AP2 (two AP2 domains) and EREBP (one AP2/ERF domain) subfamilies.
- Previous studies divided AP2 genes into AP2 and ANT clades based on phylogenetic analysis.
Purpose of the Study:
- To elucidate the molecular evolution of the AP2 subfamily.
- To investigate the evolutionary conservation of microRNA regulation in AP2 genes.
Main Methods:
- Isolation and sequencing of AP2-domain genes from gymnosperms (Cycas revoluta, Ginkgo biloba, Gnetum parvifolium) and the moss Physcomitrella patens.
- Phylogenetic analysis including green alga Chlamydomonas reinhardtii and public seed-plant gene data.
- Comparative analysis of miR172 target sites in AP2 homologs.
Main Results:
- Identified and sequenced AP2-domain genes from diverse plant lineages.
- Phylogenetic analysis revealed AP2 subfamily divergence into AP2 and ANT groups predating the last common ancestor of land plants.
- Significant conservation of miR172 target sites in gymnosperm AP2 homologs was observed, indicating conserved regulatory mechanisms.
- Gene duplications within AP2 and ANT groups occurred before the divergence of gymnosperms and angiosperms.
Conclusions:
- The AP2 subfamily's evolutionary history involves early divergence and subsequent diversification through gene duplication.
- MicroRNA-mediated gene regulation, specifically involving miR172, is an ancient mechanism conserved across land plant evolution.
- This study provides insights into the evolutionary trajectory of key plant transcription factor families and their regulatory networks.
Related Concept Videos
Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
Bacterial RNA Polymerase
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...
Exon Recombination
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Gene Duplication and Divergence
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
Protein Complexes with Interchangeable Parts
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

