The post-genomic era of interactive proteomics: Facts and perspectives

Abstract

The availability of completed genome sequences of several eukaryotic and prokaryotic species has shifted the focus towards the identification and characterization of all gene products that are expressed in a given organism. In order to cope with the huge amounts of data that have been provided by large-scale sequencing projects, high-throughout methodologies also need to be applied in the emerging field of proteomics. In this review, we discuss methods that have been recently developed in order to characterize protein interactions and their functional relevance on a large scale. We then focus on those methodologies that are suitable for the identification and characterization of protein-protein interactions, namely the yeast two-hybrid system and related methods. Several recent studies have demonstrated the power of automated approaches involving the yeast two-hybrid system in building so-called "interaction networks", which hold the promise of identifying the entirety of all interactions that take place between proteins expressed in a certain cell type or organism. We compare the yeast two-hybrid system with several other screening methods that have been developed to investigate interactions between proteins that are not amenable to conventional yeast two-hybrid screenings, such as transcriptional activators and integral membrane proteins. The eventual adaptation of such methods to a high-throughput format and their use in combination with automated yeast two-hybrid screenings will help in elucidating protein-protein interactions on a scale that would have been unthinkable just a few years ago.

Proteins Related to the Biocontrol of Pythium Damping-off in Maize with Trichoderma harzianum Rifai

“…Understanding protein functions is the primary goal in the post-genome sequence era (Auerbach et al 2002), but it must be holistic and apply to a variety of pathophysiological settings. The strong context-sensitivity of protein behavior necessitates knowledge of protein networks and their temporal-spatial dynamics in vivo, in addition to understanding the properties of individual proteins in isolation (Gygi et al 1999;James 2001).…”

Defining the Cellular Interactome of Disease-Linked Proteins in Neurodegeneration

“…The usage of the opposite fusion construct or a different protein fragment is also often effective in suppressing auto-activation. In addition, several alternative genetic screening techniques have been developed to allow the detection of interactions for transcription activators and membrane proteins (Auerbach et al, 2002).…”

A new way to explore the world of extracellular protein interactions

“…Bioinformatic studies predict that ∼20%-30% of all encoded proteins may be extracellular or membrane associated (Auerbach et al 2002a). Given the diversity of different eukaryotic cell types and the vast number of biological processes that are in some way dependent upon cell surface interactions, it is perhaps not surprising that a large proportion of eukaryotic genes may encode proteins that are either secreted or have the potential to be exposed on the outer surface of cells.…”