Jakobson Liina, Mõttus Jelena, Suurväli Jaanus, Sõmera Merike, Tarassova Jemilia, Nigul Lenne, Smolander Olli-Pekka, Sarmiento Cecilia
Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.
Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada.
Front Genet. 2024 Jun 7;15:1408665. doi: 10.3389/fgene.2024.1408665. eCollection 2024.
ATP-BINDING CASSETTE SUBFAMILY E MEMBER (ABCE) proteins are one of the most conserved proteins across eukaryotes and archaea. Yeast and most animals possess a single gene encoding the critical translational factor ABCE1. In several plant species, including and , two or more gene copies have been identified, however information related to plant gene family is still missing. In this study we retrieved gene sequences of 76 plant species from public genome databases and comprehensively analyzed them with the reference to gene (). Using bioinformatic approach we assessed the conservation and phylogeny of plant ABCEs. In addition, we performed haplotype analysis of and its paralogue using genomic sequences of 1,135 ecotypes. Plant ABCE proteins showed overall high sequence conservation, sharing at least 78% of amino acid sequence identity with AtABCE2. We found that over half of the selected species have two to eight genes, suggesting that in plants genes can be classified as a low-copy gene family, rather than a single-copy gene family. The phylogenetic trees of ABCE protein sequences and the corresponding coding sequences demonstrated that and families have independently undergone lineage-specific split of the ancestral gene. Other plant species have gained gene copies through more recent duplication events. We also noticed that ploidy level but not ancient whole genome duplications experienced by a species impacts gene family size. Deeper analysis of and from 1,135 ecotypes revealed four and 35 non-synonymous SNPs, respectively. The lower natural variation in compared to is in consistence with its crucial role for plant viability. Overall, while the sequence of the ABCE protein family is highly conserved in the plant kingdom, many plants have evolved to have more than one copy of this essential translational factor.
ATP结合盒亚家族E成员（ABCE）蛋白是真核生物和古细菌中最保守的蛋白之一。酵母和大多数动物都有一个编码关键翻译因子ABCE1的单一基因。在包括[具体植物物种1]和[具体植物物种2]在内的几种植物物种中，已经鉴定出两个或更多的ABCE基因拷贝，然而与植物ABCE基因家族相关的信息仍然缺失。在本研究中，我们从公共基因组数据库中检索了76种植物物种的ABCE基因序列，并参照拟南芥AtABCE基因（AtABCE）对它们进行了全面分析。使用生物信息学方法，我们评估了植物ABCE蛋白的保守性和系统发育。此外，我们利用1135个拟南芥生态型的基因组序列对AtABCE1及其旁系同源基因AtABCE2进行了单倍型分析。植物ABCE蛋白总体上表现出高度的序列保守性，与AtABCE2至少有78%的氨基酸序列同一性。我们发现，超过一半的所选物种有两个到八个ABCE基因，这表明在植物中ABCE基因可被归类为一个低拷贝基因家族，而不是单拷贝基因家族。ABCE蛋白序列和相应编码序列的系统发育树表明，AtABCE1和AtABCE2家族独立经历了祖先ABCE基因的谱系特异性分裂。其他植物物种通过更近的复制事件获得了ABCE基因拷贝。我们还注意到，一个物种的倍性水平而非经历的古老全基因组复制会影响ABCE基因家族大小。对1135个拟南芥生态型的AtABCE1和AtABCE2的深入分析分别揭示了4个和35个非同义单核苷酸多态性（SNP）。与AtABCE2相比，AtABCE1较低的自然变异与其对植物生存能力的关键作用相一致。总体而言，虽然ABCE蛋白家族的序列在植物界高度保守，但许多植物已经进化出不止一个拷贝的这种必需翻译因子。
