Differences in the intron-retaining fragment of the shortened isoform of the NXF1 protein in different representatives of Rodentia

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Abstract

BACKGROUND: This work is devoted to the study of the amino acid composition of the fragment of the protein translated from the intron-retaining transcript of the Nxf1 gene. The constitutive protein NXF1 is involved in the process of nuclear-cytoplasmic transport of mRNA. In addition to the constitutive NXF1 protein, there exists an isoform called sNXF1 (“s” for “short”). This isoform is a product of translation of the intron-retaining transcript. There is an early stop codon in the intronretaining transcript, so the sNXF1 protein is truncated. We have shown that the fragment of this protein corresponding to the beginning of the conserved intron exhibits evolutionary conservation.

AIM: This study aimed to analyze the species specificity of the sequence of the C-terminal fragment of the sNXF1 protein translated from the intron.

METHODS: The study was performed employed in silico methods, using the sequences of the Nxf1 gene of 33 representatives of the order Rodentia as materials, obtained from publicly available databases and NCBI data. Alignment of the nucleotide sequences was performed using the program MEGA-X, version 10.1.7, using the MUSCLE algorithm (GAP Open-400, 16 iterations). The UPGMA method was used for clustering. Further analysis was carried out using the Unipro UGENE version 36.0. program. Modeling of the protein structure was done using the SWISS-MODEL service with default settings. Phylogenetic trees were created using the Bayes Inference method in the MrBayes program and visualized using FigTree.v1.4.4. Posterior probability percentages were considered reliable if they were >80%–90%. MrBayes parameters were set in the Mesquite program. In our study, model GTR+I+G (General time reversible [GTR] was used; six types of substitution and a combination of the invariable sites model (Proportion of Invariable Sites) with a gamma-model (+I+G, rates=invgamma) were considered. To convert files between formats when performing intermediate operations, the BioEdit v.7.2.5 program was used.

RESULTS: The analysis revealed that the C-terminal fragments of the sNXF1 from some representatives of the order Rodentia are of increased length. It was found that the cause of these extended fragments in all cases was a deletion of a cytosine nucleotide. In all identified cases, regardless of the systematic position of the species, the extended fragment contains a sequence of 13 conserved amino acids.

CONCLUSION: The obtained results indicate that the analyzed sequence fragment does not influence the conformation of the protein the sNXF1 overall. However, since the fragment has a specific folding pattern, it might determine a set of RNP-complex partners.

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About the authors

Dmitrii D. Bondaruk

Saint Petersburg State University

Author for correspondence.
Email: d.bondaruk@spbu.ru
ORCID iD: 0000-0003-0265-5759
SPIN-code: 8162-8441
Russian Federation, Saint Petersburg

Elena V. Golubkova

Saint Petersburg State University

Email: e.golubkova@spbu.ru
ORCID iD: 0000-0002-9528-5760
SPIN-code: 7386-1230

Cand. Sci. (Biology)

Russian Federation, Saint Petersburg

Ludmila A. Mamon

Saint Petersburg State University

Email: lmamon46@mail.ru
ORCID iD: 0000-0001-5338-0703
SPIN-code: 7780-6907

Dr. Sci. (Biology)

Russian Federation, Saint Petersburg

Daria I. Pelle

Saint Petersburg National Research University of Information Technologies, Mechanics and Optics, University

Email: kaisa23@ya.ru
ORCID iD: 0009-0002-0025-6631
SPIN-code: 6211-7251
Russian Federation, Saint Petersburg

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Supplementary files

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2. Fig. 1. Occurrence of the NXF/NXT dimer in the highest-ranking taxa of the main evolutionary branches of the domains of life. Two clades inside Opisthokonta are marked by star symbols, Holozoa and Nucletmycea.

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3. Fig. 2. Results of the alignment of the sNXF1 fragment sequence translated from the intron 10. Different groups of sequences are marked by numbers. Parts specific to the sequences of the second group are cross-hatched. Identical fragments in the second and the third groups are circled in bold. Parts specific to the third group are marked by square mesh. Amino acid positions are counted from the first amino acid fully translated from the “cassette intron.”

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4. Fig. 3. Combined fragments of the aligned sequences of the intron-retaining transcript Nxf1 and its corresponding protein sNXF1. Deletions that result in a lengthened sNXF1 fragment translated from the intron 10 are circled. One species with a typical nucleotide sequence from each group excluding the second was chosen for ease of comprehension. Amino acid residues are counted from the first amino acid residue translated from the nucleotide sequence containing the nucleotide from the retained intron, so nucleotides are counted from the second to the last nucleotide in the exon sequence, and nucleotide positions in the cassette intron begin with the third position.

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5. Fig. 4. Comparison of the phylogenetic groups and alignment of the sNXF1 protein fragments translated from intron10.

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6. Fig. 5. Comparison of the secondary structure models of the sNXF1 protein of M. musculus (a), M. caroli (b), D. ordii (c), M. Pahari (d) and I. tridecemlineatus (e). Alpha helices are violet, beta-sheets are green, the unstructured fragment translated from the intron 10 is red.

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7. Supplement 1. Phylogenetic tree based on a full sNXF1 gene sequence of different members of Rodentia

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