In Silico Identification and Analysis of Proteins Containing the Phox Homology Phosphoinositide-Binding Domain in Kinetoplastea Protists: Evolutionary Conservation and Uniqueness of Phox-Homology-Domain-Containing Protein Architectures

Marina Petsana; Ahmed F Roumia; Pantelis G Bagos; Haralabia Boleti; Georgia G Braliou

doi:10.3390/ijms241411521

In Silico Identification and Analysis of Proteins Containing the Phox Homology Phosphoinositide-Binding Domain in Kinetoplastea Protists: Evolutionary Conservation and Uniqueness of Phox-Homology-Domain-Containing Protein Architectures

Int J Mol Sci. 2023 Jul 15;24(14):11521. doi: 10.3390/ijms241411521.

Authors

Marina Petsana^{1

2}, Ahmed F Roumia^{1

3}, Pantelis G Bagos¹, Haralabia Boleti², Georgia G Braliou¹

Affiliations

¹ Department of Computer Science and Biomedical Informatics, University of Thessaly, 2-4 Papasiopoulou Str., 35131 Lamia, Greece.
² Intracellular Parasitism Laboratory, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece.
³ Department of Agricultural Biochemistry, Faculty of Agriculture, Menoufia University, Shibin El-Kom 32514, Egypt.

Abstract

Kinetoplastea are free living and parasitic protists with unique features among Eukaryota. Pathogenic Kinetoplastea parasites (i.e., Trypanosoma and Leishmania spp.) undergo several developmental transitions essential for survival in their hosts. These transitions require membrane and cytoskeleton reorganizations that involve phosphoinositides (PIs). Phospholipids like PIs are key regulators of vital functions in all eukaryotes including signal transduction, protein transport and sorting, membrane trafficking, and cytoskeleton and membrane remodeling. A large repertoire of PI-metabolizing enzymes and PI-binding proteins/effectors carrying distinct PI-binding modules like the PX (phox homology) module could play significant roles in the life and virulence of pathogenic Kinetoplastea. The aim of this study was to retrieve the entire spectrum of Kinetoplastea protein sequences containing the PX module (PX-proteins), predict their structures, and identify in them evolutionary conserved and unique traits. Using a large array of bioinformatics tools, protein IDs from two searches (based on PFam's pHMM for PX domain (PF00787)) were combined, aligned, and utilized for the construction of a new Kinetoplastea_PX pHMM. This three-step search retrieved 170 PX-protein sequences. Structural domain configuration analysis identified PX, Pkinase, Lipocalin_5, and Vps5/BAR3-WASP domains and clustered them into five distinct subfamilies. Phylogenetic tree and domain architecture analysis showed that some domain architectures exist in proteomes of all Kinetoplastea spp., while others are genus-specific. Finally, amino acid conservation logos of the Kinetoplastea spp. and Homo sapiens PX domains revealed high evolutionary conservation in residues forming the critical structural motifs for PtdIns3P recognition. This study highlights the PX-Pkinase domain architecture as unique within Trypanosoma spp. and forms the basis for a targeted functional analysis of Kinetoplastea PX-proteins as putative targets for a rational design of anti-parasitic drugs.

Keywords: BAR domain; Kinetoplastea protists; PX domain; Pkinase domain; lipocalin domain; phosphoinositides (PIs); phylogeny; sorting nexins.

MeSH terms

Carrier Proteins* / metabolism
Eukaryota / metabolism
Humans
Phosphatidylinositols* / metabolism
Phylogeny
Signal Transduction

Substances

Phosphatidylinositols
Carrier Proteins

Grants and funding

5045902/Greece and the European Union (European Regional Development Fund), Operational Programme "Competitiveness, Entrepreneurship and Innovation" (NSRF 2014-2020)