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

BMC Molecular and Cell Biology

article

Soyfoo, Djaleel Muhammad¹  Doomah, Yussriya Hanaa²  Xu, Dong³  Zhang, Chao⁴  Sang, Huai-Ming¹  Liu, Yan-Yan¹  Zhang, Guo-Xin¹  Jiang, Jian-Xia¹  Xu, Shun-Fu¹ 

[1] Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University;Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanjing Medical University;Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri;Institute for Computational Biomedicine, Weill Cornell Medicine;Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine

关键词: Helicobacter pylori;    Vacuolating toxin a;    Bioinformatics;    Polymorphism;    Intrinsically disordered proteins;   

DOI  :  10.1186/s12860-020-00338-2

学科分类：内科医学

来源: Colegio Oficial de Psicologos

【 摘 要 】

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 < .01). Incidentally, a new region expressing sequence diversity (2 aa deletion) at the C-terminus of the p55 domain of vacA was identified during bioinformatics analysis. Prediction of secondary structures shows that the “d-region” adopts a loop conformation and is a disordered region.

【 授权许可】

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