Yeast proteomics and protein microarrays

Abstract

Our understanding of biological processes as well as human diseases has improved greatly thanks to studies on model organisms such as yeast. The power of scientific approaches with yeast lies in its relatively simple genome, its facile classical and molecular genetics, as well as the evolutionary conservation of many basic biological mechanisms. However, even in this simple model organism, systems biology studies, especially proteomic studies had been an intimidating task. During the past decade, powerful high-throughput technologies in proteomic research have been developed for yeast including protein microarray technology. The protein microarray technology allows the interrogation of protein-protein, protein-DNA, protein-small molecule interaction networks as well as post-translational modification networks in a large-scale, high-throughput manner. With this technology, many groundbreaking findings have been established in studies with the budding yeast Saccharomyces cerevisiae, most of which could have been unachievable with traditional approaches. Discovery of these networks has profound impact on explicating biological processes with a proteomic point of view, which may lead to a better understanding of normal biological phenomena as well as various human diseases.

Graphical abstract

Fig. 1

Application of functional protein microarray and novel insights gained in protein interaction and modification. Protein–protein interactions may be detected with either fluorophore-labeled proteins or specific recognition antibodies to the probe protein. Protein–nucleic acid interactions can be visualized with fluorophore-labeled DNA/RNA. Protein–small molecule interactions may be identified with biotinylated small molecules and fluorophore-labeled streptavidin. Posttranslational modifications of proteins are not drawn to scale. P, phosphorylation; U, ubiquitination; Ac, acetylation.

Fig. 2

Manufacture and application of functional protein microarrays. Functional protein microarrays can either be manufactured by printing a library of in vitro or in vivo expressed, affinity-purified proteins on to coated glass slides with a microarray printer (top), or printing the protein expression plasmids on to the slides followed by on-slide in vitro expression (bottom). The printed microarrays are then ready for various downstream applications, such as protein–protein/DNA/small molecule interaction and protein post-translational modification studies.

Fig. 3

Schematic diagram for protein kinase target identification, consensus phosphorylation motif identification and determination.

Fig. 4

Comprehensive understanding of biological processes through integrated information of biological systems and environmental factors.