New genotypes of Helicobacter Pylori VacA d-region identified from global strains

• Published in: BMC cell biology 2021-01, Vol.22 (1), p.4-4, Article 4
• Main Authors: Soyfoo, Djaleel Muhammad, Doomah, Yussriya Hanaa, Xu, Dong, Zhang, Chao, Sang, Huai-Ming, Liu, Yan-Yan, Zhang, Guo-Xin, Jiang, Jian-Xia, Xu, Shun-Fu
• Format: Article
• Language: English
• Subjects: Amino acids; Bioinformatics; C-Terminus; Cancer; Confidence intervals; Conformation; Development and progression; Disease; Genetic aspects; Genetic diversity; Genotype & phenotype; Genotypes; Health aspects; Helicobacter; Helicobacter infections; Helicobacter pylori; Identification and classification; Intrinsically disordered proteins; Nucleotide sequence; Physicochemical properties; Polymorphism; Protein structure; Proteins; Secondary structure; Strains (organisms); VacA protein; Vacuolating toxin a
• ISSN: 2661-8850; 2661-8850; 1471-2121
• DOI: 10.1186/s12860-020-00338-2

Pathogenesis of Helicobacter Pylori (HP) vacuolating toxin A (vacA) depends on polymorphic diversity within the signal (s), middle (m), intermediate (i), deletion (d) and c-regions. These regions show distinct allelic diversity. The s-region, m-region and the c-region (a 15 bp deletion at the 3'-end region of the p55 domain of the vacA gene) exist as 2 types (s1, s2, m1, m2, c1 and c2), while the i-region has 3 allelic types (i1, i2 and i3). The locus of d-region of the vacA gene has also been classified into 2 genotypes, namely d1 and d2. We investigated the "d-region"/"loop region" through bioinformatics, to predict its properties and relation to disease. One thousand two hundred fifty-nine strains from the NCBI nucleotide database and the dryad database with complete vacA sequences were included in the study. The sequences were aligned using BioEdit and analyzed using Lasergene and BLAST. The secondary structure and physicochemical properties of the region were predicted using PredictProtein. We identified 31 highly polymorphic genotypes in the "d-region", with a mean length of 34 amino acids (9 ~ 55 amino acids). We further classified the 31 genotypes into 3 main types, namely K-type (strains starting with the KDKP motif in the "d-region"), Q-type (strains starting with the KNQT motif), and E-type (strains starting with the ESKT motif) respectively. The most common type, K-type, is more prevalent in cancer patients (80.87%) and is associated with the s1i1m1c1 genotypes (P