The Streptococcal Proteome

Excerpt

The nucleotide sequence of the Streptococcus pyogenes genome was first determined in 2001, which inferred a proteome of 1,752 proteins (Ferretti, et al., 2001). The genomic sequencing of additional isolates showed that all streptococcal chromosomes are poly-lysogenized with bacteriophages (Sumby, Whitney, Graviss, DeLeo, & Musser, 2006), which account for approximately 10% of their genome content (Ferretti, et al., 2001). The number and types of prophages that are present in the genomes of different clinical isolates varies significantly, which suggests a stochastic process of co-evolution (Canchaya, Fournous, & Brüssow, 2004). Horizontally transmitted integrative conjugative elements, transposons, and insertion sequences also contribute to genomic variation within the species. Due to the extent of horizontal DNA transmission, S. pyogenes is thought to have a theoretically infinite pan-genome and—by extension—a theoretically infinite proteome (Desiere, McShan, van Sinderen, Ferretti, & Brüssow, 2001). Moreover, multiple protein isoforms can be derived from a single open reading frame (ORF) following post-translational modifications, such as truncation or phosphorylation, and each isoform may have a unique function. As a result, the complexity of an organism’s proteome is estimated to be at least two to three orders of magnitude greater than that of the genome (Figure 1) (Matthiesen & Jensen, 2008; Cain, Solis, & Cordwell, 2014).

The availability of the genome sequence of S. pyogenes and advances in mass spectrometry (MS) have greatly enhanced our ability to characterize proteins on a genome-wide scale. Proteomic studies of S. pyogenes have been motivated by the pursuit of answers to fundamental questions, such as: How are proteins trafficked to specific sub-cellular locations? What is the functional significance of protein localization? How does the proteome transition in response to changing conditions encountered in the host? What are the differences between streptococci associated with a localized infection, as compared to those associated with life-threatening invasive infections? What are the functional significances of interactions between streptococcal proteins and human host proteins? What physiologic changes in the proteome occur in response to the presence of antimicrobials? What are correlates of protective immunity? What Streptococcal proteins can be used to vaccinate against disease? What proteins elicit pathogenic antibodies? Answering these questions is important in developing new approaches to mitigate the morbidity and mortality associated with S. pyogenes.

In this chapter, we focus on the advances in our understanding of the S. pyogenes proteome from the perspective shaped by results obtained using proteomics, or studies that have simultaneously characterized a set of proteins. We start by describing the methods that have been used to study the proteome and then discuss how these approaches have led to insights into the pathogen’s response to changing conditions, circumvention of the immune response, and the organization and regulation of extracellular proteins. Finally, we will review advances in identifying proteins that evoke auto- and protective immunity. Given the rapid pace at which various aspects of proteomic investigation are progressing, including instrumentation, workflow strategies, and bioinformatics, the characterization of the S. pyogenes proteome is, in many ways, just beginning.