20201005 Applications Of Top Down Proteomics ((NEW))

Exportomes have fundamental roles in apicomplexan parasite survival and virulence, but studies on the Babesia exportome have lagged behind. The recent completion of genome databases for multiple Babesia species and the development of transfection tools (reviewed in [85]) have allowed us to begin to describe Babesia exportomes. Several proteins have been identified from bioinformatic or proteomics approaches and verified by expression of the tagged candidate proteins. However, the proteins responsible for ridge formation, modification of the iRBCs cytoskeleton, and transport to the surface of iRBCs have not been identified. Trafficking of integral proteins such as VESA1 and mtm across the parasite plasma membrane likely require protein refolding, which could be performed by parasite-encoded chaperones (Schematic of the protein export pathway is summarized in Fig 5). While P. falciparum has an expanded chaperone repertoire containing the domain DNAJ, of which some members are exported to RBCs [86], similar proteins have not been found in Babesia. PLM have been identified in hundreds of Babesia proteins including all currently known spherical body proteins, which are exportome proteins. Thus, PLM is a powerful tool to predict the Babesia exportome. However, some of the experimentally confirmed proteins do not possess a PLM (Table 1), and it is unclear whether PLM in the middle or at C-terminus of the proteins are functional. Further intensive studies using in silico analysis and proteomics will be necessary, and classical approaches such as proteomic analysis of spherical bodies may be also useful. Studies in Plasmodium and Toxoplasma have shown that dense granule proteins are responsible for host cell modification, and similarly, most of the experimentally confirmed Babesia proteins are deposited in spherical bodies and routed to the host RBC. Genetic manipulation tools such as genome editing and inducible gene knockdown/knockout system will be helpful to characterize the functions of proteins identified by in silico screens or proteomics.

20201005 Applications of Top Down Proteomics

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