Exoproteomics: exploring the world around biological systems

Abstract

The term 'exoproteome' describes the protein content that can be found in the extracellular proximity of a given biological system. These proteins arise from cellular secretion, other protein export mechanisms or cell lysis, but only the most stable proteins in this environment will remain in abundance. It has been shown that these proteins reflect the physiological state of the cells in a given condition and are indicators of how living systems interact with their environments. High-throughput proteomic approaches based on a shotgun strategy, and high-resolution mass spectrometers, have modified the authors' view of exoproteomes. In the present review, the authors describe how these new approaches should be exploited to obtain the maximum useful information from a sample, whatever its origin. The methodologies used for studying secretion from model cell lines derived from eukaryotic, multicellular organisms, virulence determinants of pathogens and environmental bacteria and their relationships with their habitats are illustrated with several examples. The implication of such data, in terms of proteogenomics and the discovery of novel protein functions, is discussed.

Comparative genomic, proteomic and exoproteomic analyses of three Pseudomonas strains reveals novel insights into the phosphorus scavenging capabilities of soil bacteria

“…Characterizing the exoproteomes, and thus the functional entities associated with environmental interactions (Armengaud et al ., 2012), of various Pseudomonas strains allowed us to deepen our understanding of Pi‐regulated protein expression in this genus (Figs. 3 and 4).…”

“…Exoproteomics captures the extracellular protein fraction that results from active secretion, cell lysis or leakage during cell division (Armengaud et al ., 2012; Ebner et al ., 2016). Removing the cellular fraction prior to protein extraction can help to identify exoproteins that are involved in the interaction of microorganisms with their environment (Christie‐Oleza et al ., 2012, 2015).…”

Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes

“…The identification of thse biomarkers have shed new light on the physiological and biochemical traits that are unique to each species and its ecological microniche. In particular, the Mm exoproteome was almost as dominant as the cellular proteome, which hinders a deeper proteomic view (Armengaud et al, 2012). Undoubtedly, much of the future progress in Figure 2 Schematic view of the Geodermatophilaceae physiological determinants.…”

Functional distinctness in the exoproteomes of marine Synechococcus

“…It comprises actively exported proteins and those that are released by cell lysis or leakage. For example, the exoproteomes of pure cultures are those proteins that can be detected after purification from the culture medium once cells have been removed (Armengaud et al ., 2012). These proteins, present in hostile extracellular conditions, need long half‐lives in order to accumulate and, hence, be detected.…”