Abstract
HUA ENHANCER 1 (HEN1) is a pivotal mediator in protecting sRNAs from 3′-end uridylation and 3′ to 5′ exonuclease-mediated degradation in plants. Here, we investigated the pattern of the HEN1 protein family evolutionary history and possible relationships in the plant lineages using protein sequence analyses and conserved motifs composition, functional domain identification, architecture, and phylogenetic tree reconstruction and evolutionary history inference. According to our results, HEN1 protein sequences bear several highly conserved motifs in plant species retained during the evolution from their ancestor. However, several motifs are present only in Gymnosperms and Angiosperms. A similar trend showed for their domain architecture. At the same time, phylogenetic analysis revealed the grouping of the HEN1 proteins in the three main super clads. In addition, the Neighbor-net network analysis result provides some nodes have multiple parents indicating a few conflicting signals in the data, which is not the consequence of sampling error, the effect of the selected model, or the estimation method. By reconciling the protein and species tree, we considered the gene duplications in several given species and found 170 duplication events in the evolution of HEN1 in the plant lineages. According to our analysis, the main HEN1 superclass mostly showed orthologous sequences that illustrate the vertically transmitting of HEN1 to the main lines. However, in both orthologous and paralogs, we predicted insignificant structural deviations. Our analysis implies that small local structural changes that occur continuously during the folds can moderate the changes created in the sequence. According to our results, we proposed a hypothetical model and evolutionary trajectory for the HEN1 protein family in the plant kingdom.
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239_2023_10109_MOESM1_ESM.txt
Supplementary file1 (TXT 404 kb). Supplementary file 1: The HEN1 homologous sequences from the plant species considered for this study
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Supplementary file2 (CLANS 1786 kb). Supplementary file 2: The constructed file of sequence-similarity-based grouping of the HEN1 protein family dataset by CLANS
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Supplementary file3 (TXT 287 kb). Supplementary file 3: The predicted functional domains using querying the protein sequence in the Hmmscan search tool (https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan) against the Pfam database (http://pfam.xfam.org/)
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Supplementary file4 (PDF 993 kb). Supplementary file 4: The unrooted phylogenetic tree of the HEN1 protein sequences was rooted with the outlier (outgroup Marchantia paleacea HEN1 protein sequence (KAG6553076.1)). Evolutionary analyses were conducted in MEGA11 and visualized by iTOL v5 online tool. In addition, graphical representation of the conserved motifs (B)/domains (C) variations and their architecture in the Plant HEN1 protein sequence and their evolutionary relationship within each HEN1 protein clade. The protein motifs were obtained using MEME suite (http://memesuite.org/) and the functional domains were predicted by querying the protein sequence in the Hmmscan search tool (https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan) against the Pfam database (http://pfam.xfam.org/). Different motifs were represented by different colored boxes and the consensus sequences of the motifs are listed. The domains are marked with different shapes and colors
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Supplementary file5 (PDF 190 kb). Supplementary file 5: Gene duplications were identified by searching for all branching points in the topology with at least one species that is present in both subtrees of the branching point. Evolutionary analyses were conducted in MEGA11
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Supplementary file6 (PDB 566 kb). Supplementary File 6: The predicted PDB files for 20 HEN1selected proteins from the oldest extant land plant lineages to those present in modern HEN1 in angiosperms considered for this study
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Hajieghrari, B., Niazi, A. Phylogenetic and Evolutionary Analysis of Plant Small RNA 2′-O-Methyltransferase (HEN1) Protein Family. J Mol Evol 91, 424–440 (2023). https://doi.org/10.1007/s00239-023-10109-0
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DOI: https://doi.org/10.1007/s00239-023-10109-0