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High‐throughput screening for hypothetical proteins in Salmonella typhimurium by affinity proteoimcs

Recently human genome project has identified a large number of open reading frames in many species, whose functions are not known. Those genes are annotated as hypothetical, unknown, or uncharacterized proteins. Quite often there is no experimental evidence even for the expression of the hypothetical proteins, although their existence has been predicted by bioinformatics tools. Nucleotides serve as structural units of RNA and DNA and also as important cofactors in cellular signaling pathways and metabolism. In this study several affinity ligands such as ADP, ATP, GTP, and NAD(P)+ were utilized for isolation of nucleotide(s)‐binding proteins in Salmonella typhimurium. Those binding proteins were identified by MALDI‐TOF MS and shotgun analysis. Fourteen proteins, as ATP‐binding proteins, were identified as hypothetical proteins. Six proteins among GTP‐binding proteins were also hypothetical proteins. Furthermore, 17 NAD(P)+‐binding proteins were hypothetical. These results suggest that affinity proteomics will be very effective for high‐throughput screening for hypothetical proteins. [This work has been supported by Ministry of Education and Science, Korea.]