Interactome Mapping: Using Protein Microarray Technology to Reconstruct Diverse Protein Networks

Uzoma, Ijeoma; Zhu, Heng

The capabilities of microarray technology are further expanding with the development of label-free optical tech- Figure 2 Reconstituted interaction networks in cellular systems generated through protein microarray studies Interaction mapping with protein microarrays has been applied to numerous organisms to achieve diverse representations of molecular networks. A. Li et al. probed a human transcription factor (TF) microarray with four conserved kinases encoded by herpesviruses to reveal the host targets of the viral kinases [35] . Verified interactions between the viral target host proteins are shown. B. Using a yeast proteome microarray, Lu et al. identified the substrates of the HECT E3 ligase Rsp5 [22] . Through gene ontology analysis Rsp5 was linked to subgroups of substrates based on function. C. The A. thaliana MAP kinase signaling network was reconstructed using an Arabidopsis protein microarray [15] (adapted with permission from Dr. Savithramma P. Dinesh-Kumar). The hierarchical phosphorylation network depicts the MKKs (upper nodes), MPKs (middle nodes) and substrates (bottom nodes). D. DNA binding specificity of unconventional DNA-binding proteins (uDBPs) was characterized using the TF microarray [18] . The uDBPs are clustered based on target sequence similarity and proteins of different functional classes are color-coded. ''C'' denotes consensus sequences for each sub-branch are shown. E. The E. coli proteome microarray was used to identify differentially immunogenic proteins between HC and CD patient samples depicted in the heat map [8] . The yellow and blue colors indicate high and low immunogenic responses, respectively. HC, healthy controls; CD, Crohn's disease.