Barros Nicolle Louise Ferreira, Filgueiras João Pedro Carmo, Trenz Thomaz Stumpf, Weber Guilherme, Turchetto-Zolet Andreia Carina, Margis-Pinheiro Marcia
Programa de Pós-graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
Front Mol Biosci. 2025 Jun 13;12:1456645. doi: 10.3389/fmolb.2025.1456645. eCollection 2025.
ABA, Stress, and Ripening (ASR) proteins are characterized by the presence of the ABA/WDS domain and are involved in plant development processes and tolerance to abiotic and biotic stresses. Despite their importance as transcription factors or molecular chaperones, a complete understanding of their biological roles is limited by a lack of information on their mechanisms of action, protein structure, and evolutionary relationships between family members. Our previous molecular dynamics simulation analysis of rice OsASR5 suggested that H, R, H, and K, are the main residues involved in the interaction with DNA, essential for the transcription factor activity of this protein. However, the presence and conservation of the DNA-binding domain among ASR family members remain unknown. Likewise, there is a lack of phylogenetic analyses evaluating the evolutionary history of ASR proteins across major taxonomic groups, outside just the species.
To address these gaps, we conducted a phylogenetic study and protein sequence analyses to gain insights into the evolution of ASR genes in plants. We performed a genome-wide identification of ASR genes via HMMER, using the ABA/WDS domain, in 163 Archaeplastida genomes.
Our results reveal that the potential origin of the ASR gene occurred in the common ancestor of Streptophytes (Charophytes and Embryophytes). Moreover, our study identifies ASR genes in seedless plants. The evolutionary relationship between 465 ASR homologs, found in 76 species, was estimated through maximum likelihood analysis. The results reinforce the rapid and dynamic evolution of the ASR gene family, reflected by the low support in the deep nodes of the phylogeny and the great variation in the number of ASRs in the genomes evaluated, and in some cases their complete absence. As for diversification, tandem duplications seem to be the main mechanism involved. Regarding the conservation of residues in the domain, only two of the 78 are widely conserved, such as E and H. By analyzing the three-dimensional model, we noticed the interaction between them and we hypothesize that they are essential for the stabilization of the domain during interaction with DNA.
脱落酸、胁迫与成熟（ASR）蛋白的特征是含有脱落酸/ WD40结构域，参与植物发育过程以及对非生物和生物胁迫的耐受性。尽管它们作为转录因子或分子伴侣很重要，但由于缺乏关于其作用机制、蛋白质结构以及家族成员之间进化关系的信息，对其生物学作用的全面理解受到限制。我们之前对水稻OsASR5的分子动力学模拟分析表明，组氨酸（H）、精氨酸（R）（原文此处可能有误，推测应为其他氨基酸）、组氨酸（H）和赖氨酸（K）是与DNA相互作用的主要残基，对该蛋白的转录因子活性至关重要。然而，ASR家族成员中DNA结合结构域的存在和保守性仍然未知。同样，除了少数物种外，缺乏评估主要分类群中ASR蛋白进化历史的系统发育分析。
为了填补这些空白，我们进行了系统发育研究和蛋白质序列分析，以深入了解植物中ASR基因的进化。我们使用HMMER通过脱落酸/ WD40结构域在163个古质体基因组中进行了全基因组范围内的ASR基因鉴定。
我们的结果表明，ASR基因的潜在起源发生在链形植物（轮藻和胚植物）的共同祖先中。此外，我们的研究在无籽植物中鉴定出了ASR基因。通过最大似然分析估计了在76个物种中发现的465个ASR同源物之间的进化关系。结果强化了ASR基因家族的快速和动态进化，这体现在系统发育树深层节点的支持度较低以及所评估基因组中ASR数量的巨大差异，在某些情况下甚至完全没有。至于多样化，串联重复似乎是主要涉及的机制。关于结构域中残基的保守性，78个残基中只有两个广泛保守，如谷氨酸（E）和组氨酸（H）。通过分析三维模型，我们注意到它们之间的相互作用，并假设它们在与DNA相互作用期间对结构域的稳定至关重要。
