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A Large Scale Analysis of Protein–Protein Interactions in the Nitrogen-fixing Bacterium Me.pdf

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A Large Scale Analysis of Protein–Protein Interactions in the Nitrogen-fixing Bacterium Me

A Large Scale Analysis of Protein–Protein Interactions in the Nitrogen-fixing Bacterium Mesorhizobium loti Yoshikazu SHIMODA, Sayaka SHINPO, Mitsuyo KOHARA, Yasukazu NAKAMURA, Satoshi TABATA,, and Shusei SATO* Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan (Received 19 October 2007; accepted on 2 December 2007) Abstract Global viewing of protein–protein interactions (PPIs) is a useful way to assign biological roles to large numbers of proteins predicted by complete genome sequence. Here, we systematically analyzed PPIs in the nitrogen-fixing soil bacterium Mesorhizobium loti using a modified high-throughput yeast two-hybrid system. The aims of this study are primarily on the providing functional clues to M. loti proteins that are relevant to symbiotic nitrogen fixation and conserved in other rhizobium species, especially proteins with regulatory functions and unannotated proteins. By the screening of 1542 genes as bait, 3121 inde- pendent interactions involving 1804 proteins (24% of the total protein coding genes) were identified and each interaction was evaluated using an interaction generality (IG) measure and the general features of the interacting partners. Most PPIs detected in this study are novel interactions revealing potential func- tional relationships between genes for symbiotic nitrogen fixation and signal transduction. Furthermore, we have predicted the putative functions of unannotated proteins through their interactions with known proteins. The results described here represent new insight into protein network of M. loti and provide useful experimental clues to elucidate the biological function of rhizobial genes that can not be assigned directly from their genomic sequence. Key words: Mesorhizobium loti; Protein–protein interaction; Yeast two-hybrid system 1. Introduction Bacteria belonging to the family Rhizobiaceae (rhi- zobia) are biologically unique organisms that exhibit two distinct lifestyles in nature, as