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Updated: Dec 7, 2025
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
Identification and analysis of micro-exons in AP2/ERF and MADS gene families
Qi Song1,2, Amna Bari1,2, Huan Li1,2
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
Abstract:
Micro-exons are a set of ultrashort exons with lengths ≤ 51 nucleotides. Our previous study revealed that micro-exons were enriched in AP2 domains and K-box domains, which are crucial components of AP2/ERF (APETALA2/ethylene-responsive element-binding protein) and MADS-box (an acronym of MCM1, AGAMOUS, DEFICIENS and SRF) genes, respectively. In this study, we analyzed micro-exons in the AP2/ERF family from 63 species and demonstrated that 76.8% of micro-exons are concentrated in AP2 domains. Most micro-exons appeared in the AP2 subfamily of all the terrestrial plants, but not algae. In addition, micro-exons and AP2 domains are conserved and under negative selection. The MIKC gene is a typical MADS-box gene family in terrestrial plants and includes one MADS-box domain and one K-box domain. A total of 92.3% of micro-exons were observed in K-box domains, and two micro-exons usually encoded a region of K-box domain, which is the key to MADS-box protein polymerization. Furthermore, the micro-exons of the K-box domain had higher ratios of nonsynonymous mutations than those of the AP2 domains. Overall, here we explored the relationships and differences among micro-exons in AP2/ERF and MADS families, and revealed potential functional roles of micro-exons in these domains.
Insights
Micro-exons, ultrashort gene segments, are concentrated in AP2/ERF and MADS-box gene domains in terrestrial plants. These micro-exons are conserved and play key roles in protein structure and function.
Area of Science:
- Genomics
- Molecular Biology
- Evolutionary Biology
Background:
- Micro-exons are defined as ultrashort exons (≤51 nucleotides).
- Previous research indicated micro-exon enrichment in APETALA2/ethylene-responsive element-binding protein (AP2/ERF) and MADS-box gene domains.
- AP2/ERF and MADS-box genes are critical for plant development.
Purpose of the Study:
- To analyze micro-exons within the AP2/ERF gene family across 63 species.
- To investigate the conservation and evolutionary pressures on micro-exons and AP2 domains.
- To compare micro-exon characteristics between AP2/ERF and MADS-box gene families.
Main Methods:
- Bioinformatic analysis of micro-exon distribution in AP2/ERF genes from 63 plant species.
- Comparative analysis of micro-exon presence in AP2 and K-box domains.
- Assessment of conservation and selection pressures (negative selection) on micro-exons and domains.
- Analysis of mutation rates in micro-exons within K-box and AP2 domains.
Main Results:
- 76.8% of micro-exons in the AP2/ERF family are located within AP2 domains.
- Micro-exons are prevalent in the AP2 subfamily of terrestrial plants but absent in algae.
- Micro-exons and AP2 domains exhibit conservation and are under negative selection.
- 92.3% of micro-exons were found in K-box domains of MADS-box genes, often encoding key polymerization regions.
- K-box micro-exons showed higher nonsynonymous mutation rates compared to AP2 micro-exons.
Conclusions:
- Micro-exons are significant components of AP2/ERF and MADS-box gene families in terrestrial plants.
- The distribution and conservation suggest functional importance in these gene domains.
- Differences in mutation rates highlight distinct evolutionary dynamics between micro-exons in AP2 and K-box domains.
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