Technologies for Proteome-Wide Discovery of Extracellular Host-Pathogen Interactions

Martinez-Martin, Nadia

Proteins and Interacting Partners. The proteins expressed on the surface of pathogens mediate functions necessary for survival, replication, immunoevasion, and transmission and therefore are logical candidates for therapeutic and vaccine design. However, the study of the surface proteome in pathogens, particularly in bacteria is constrained by the fact that commonly used prediction algorithms fail to correctly predict the location of several proteins [29, [99] [100] [101] . Despite the characterization of the extracellular proteins and their interactions still representing the Achilles heel of most proteomics methods, MS has emerged as an invaluable approach to characterize the protein composition of plasma membranes [5] . To date, several studies have exploited MS-based techniques to gain insights into the extracellular protein composition of bacterial pathogens [101] [102] [103] [104] . For example, Palmer and colleagues studied the surface proteome of the tick-borne intracellular pathogen Anaplasma marginale (Rickettsiales: Anaplasmataceae) using liquid chromatography and tandem MS [105] . Interestingly, the authors found that the surface proteome of A. marginale isolated from tick cells, despite being less complex than that of bacteria isolated from human erythrocytes, contained a novel protein, which the authors hypothesized to play a function in human cell invasion in spite of its human counterreceptor remaining uncharacterized. This interesting observation suggests a remodeling of the bacteria surface proteome during the transition between mammalian and arthropod hosts, an aspect of the infection that could be targeted to block transmission. Similarly, several studies have pursued the identification of the proteins present in viral particles utilizing MS. Although these analyses suffer from several drawbacks associated with membrane protein characterization, particularly the poor solubility of these proteins and the low abundance of many plasma membrane proteins, these studies have revealed a complex composition for most of the viruses studied, alongside incorporation of many host proteins in the virions, in most cases with undetermined functions [106] [107] [108] . An interesting observation from some of the studies referred above is the fact that certain bacterial proteins, predicted cytoplasmic by consensus, can be found in the extracellular environment of the cell, where they may play alternative functions. In fact, the number of proteins that are secreted through noncanonical signal sequence pathways is increasingly appreciated [99, 100, 109, 110] . Little is known about these bacterial proteins originally described as cytosolic proteins but capable of exerting functions on the cell surface, which some authors have named moonlight proteins, in reference to their potential to exert multiple functions [111] . There is emerging evidence that protein moonlighting contributes to virulence of important bacterial pathogens including Staphylococcus aureus or Mycobacterium tuberculosis, sometimes in fascinating ways. For example, M. tuberculosis is known to encode two molecular chaperones, Cpn60.1 and Cpn60.2, which function as modulators of myeloid cells among other regulatory functions [112] . Despite these chaperones being by definition cytosolic, Cnp60.2 has been detected in significant amounts on the bacterial surface, and either recombinant Cnp60.2 or antibodies against this protein efficiently block binding of M. tuberculosis