Bioinformatics analysis of ubiquitin expression protein gene from Heterodera latipons

• Published in: Saudi journal of biological sciences Vol. 26; no. 7; pp. 1463 - 1467
• Main Authors: Al-Banna, Luma, Sadder, Monther T., Lafi, Hamzeh A., Dawabah, Ahmed A.M., Al-Nadhari, Saleh N.
• Format: Journal Article
• Language: English
• Published: Riyadh, Saudi Arabia Elsevier B.V 01.11.2019; Saudi Biological Society; Elsevier
• Subjects: DNA; Mediterranean cereal cyst nematode; Nucleotide; Protein; البروتينات; التعبير الجيني; المعلوماتية الحيوية; اليوبيكويتين; Nucleotide; DNA; Mediterranean cereal cyst nematode; Protein
• ISSN: 1319-562X; 2213-7106
• DOI: 10.1016/j.sjbs.2018.06.005

Ubiquitin expression protein DNA clone (Hl-UBI) was isolated from Heterodera latipons collected from North Jordan. Its sequence of 285 nucleotides was also determined and deposited in the GeneBank. The 285-bp open reading frame coded for 76-amino acid protein having two domains; the ubiquitin domain and the C terminal extension. The first 59 amino acids were predicted with the ubiquitin domain with identity percentages of 78% to ubiquitin of H. schachtii, 77% to polyubiquitin of Globodera pallida, 74% to ubiquitin of Globodera rostochiensis and 72% to ubiquitin of Heterodera glycines. The other domain at the C-terminus, containing 17 amino acids, showed no homology to any known protein. Sequence analysis showed a calculated encoding amino acids molecular weight of 8.77 kDa, theoretical isoelectric point = 4.76, negatively charged residues = 12, positively charged residues = 9, extinction coefficient = 1490, estimated half-life = 30 h, instability index = 32.51 and grand average of hydropathicity = −0.537. The demonstrated subcellular localization analysis of cytoplasm, cell nucleus, mitochondrion, cell skeleton and plasma membrane of Hl-UBI protein occupied about 52.20, 21.70, 17.40, 4.30 and 4.30%, respectively. Sequence, homology and structural analysis confirmed that Hl-UBI gene was highly conserved during evolution and belonged to ubiquitin gene family.