Bioinformatics analysis of ubiquitin expression protein gene from Heterodera latipons

Luma Al-Banna; Monther T Sadder; Hamzeh A Lafi; Ahmed A M Dawabah; Saleh N Al-Nadhari

doi:10.1016/j.sjbs.2018.06.005

Bioinformatics analysis of ubiquitin expression protein gene from Heterodera latipons

Saudi J Biol Sci. 2019 Nov;26(7):1463-1467. doi: 10.1016/j.sjbs.2018.06.005. Epub 2018 Jun 27.

Authors

Luma Al-Banna¹, Monther T Sadder², Hamzeh A Lafi³, Ahmed A M Dawabah⁴, Saleh N Al-Nadhari³

Affiliations

¹ Department of Plant Protection, Faculty of Agriculture, The University of Jordan, Amman, Jordan.
² Department of Horticulture and Crop Science, Faculty of Agriculture, The University of Jordan, Amman, Jordan.
³ Department of Plant Protection, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia.
⁴ Nematode Diseases Research Department, Plant Pathology Research Institute, Agricultural Research Center, 9 Gamaa Street, Giza 12619, Egypt.

Abstract

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.

Keywords: DNA; Mediterranean cereal cyst nematode; Nucleotide; Protein.