Abstract:
In order to obtain the porcupine MITF-M transcription sequence and conduct bioinformatics analysis, in this experiment, total RNA was extracted from the auricular-skin tissue samples of artificially reared porcupine and transcriptome sequencing performed without reference. All the obtained MITF gene transcripts were screened by sequence alignment analysis for porcupine MITF-M transcripts. Then, the physicochemical properties, amino acid composition, subcellular localization, secondary structure, tertiary structure, signal peptide and transmembrane region of the protein encoded by the porcupine MITF-M gene were predicted and analyzed by bioinformatics online software. Finally, the homology of MITF-M protein between porcupine and 9 species such as Rattus norvegicus, Gallus gallus and Ovis aries was analyzed. Neighbor-joining(NJ) method was used to construct the phylogenetic tree of MITF-M protein. The results showed that the transcription sequence of MITF-M of porcupine(uploaded to GenBank, entry number is MW84037) was 4 772 bp, containing 9 exons, and CDS length was 1 260 bp(229-1 488 bp), encoding 419 amino acids. The molecular formula of porcupine MITF-M protein was C
2010H
3263N
585O
652S
26, consisting of 6 536 atoms. The relative molecular weight was 46 890.11. The theoretical isoelectric point was 5.82, which was acidic protein. The amino acid coefficient of fat was 79.64, the instability index was 69.40, and the hydrophilic index was-0.617. Porcupine MITF-M protein was composed of 20 amino acids, among which leucine was the highest, accounting for 11.5%, while tryptophan was the lowest, accounting for only 0.2%. The number of amino acid residues with positive(aspartic acid, glutamic acid) and negative(arginine, lysine) charges was 52 and 44, respectively. The secondary structure was composed of α-helix, extension chain, β-rotation and random curl, of which the α-helix accounted for 37.47%; the extension chain accounted for 7.40%; the β-rotation accounted for 2.86%, and the random curl accounted for 52.27%. There was a left-right symmetric CLEAR-box structure in the tertiary structure. Porcupine MITF-M protein had no signal peptide and no transmembrane region. The amino acid sequence of porcupine MITF-M protein was the most similar to human MITF-M protein(95.7%). Porcine MITF-M protein had the lowest variation(4.2%). The porcupine was the closely evolutionary relative to the Rattus norvegicus and Mus musculus, fitting the species taxonomy. The results indicated that the porcupine MITF-M transcript sequence was successfully obtained, and its encoded protein was consistent with the structural characteristics of the transcription factor playing a role in the nucleus.