Di-myo-inositol 1,1 -phosphate (DIP) is a major osmoprotecting metabolite in a number of hyperthermophilic species of archaea and bacteria. Although the DIP biosynthesis pathway was previously proposed, genes encoding only two of the four required enzymes, inositol-1-phosphate synthase and inositol monophosphatase, were identified. In this study we used a comparative genomic analysis to predict two additional genes of this pathway (termed dipA and dipB) that remained missing. In Thermotoga maritima both candidate genes (in an originally misannotated locus TM1418) form an operon with the inositol-1-phosphate synthase encoding gene (TM1419). A predicted inositol-monophosphate cytidylyltransferase activity was directly confirmed for the purified product of T. maritima gene dipA cloned and expressed in Escherichia coli. The entire DIP pathway was reconstituted in E. coli by cloning of the TM1418 -TM1419 operon in pBAD expression vector and confirmed to function in the crude lysate. 31 P NMR and MS analysis revealed that DIP synthesis proceeds via a phosphorylated DIP intermediate, P-DIP, which is generated by the dipBencoded enzyme, now termed P-DIP synthase. This previously unknown intermediate is apparently converted to the final product, DIP, by an inositol monophosphatase-like phosphatase. These findings allowed us to revise the previously proposed DIP pathway. The genomic survey confirmed its presence in the species known to use DIP for osmoprotection. Among several newly identified species with a postulated DIP pathway, Aeropyrum pernix was directly proven to produce this osmolyte.comparative genomics ͉ di-myo-inositol-1,3-phosphate biosynthesis ͉ Thermotoga maritima T he most common mechanism of osmoadaptation in microorganisms involves the accumulation of specific organic osmolytes, so-called compatible solutes, amino acids, sugars, and polyols, that can be taken up from the environment or synthesized de novo (1-3). In thermophiles and hyperthermophiles, compatible solutes are generally different from those found in mesophiles (4), and many of them additionally contribute to thermoprotection.Di-myo-inositol 1,1Ј-phosphate (DIP) is one of the major compatible solutes in a number of thermophilic archaea of the genera Pyrococcus, Methanococcus, Thermococcus, and Archaeoglobus and bacteria belonging to the genera Aquifex, Rubrobacter, and Thermotoga, including Thermotoga maritima and Thermotoga neapolitana (4-7). DIP levels are highly increased at supraoptimal growth temperatures in both Methanococcus igneus and Thermotogales, suggesting that this solute also plays a thermoprotective role (6,8).Based on the study in M. igneus (9) and the reported stereochemistry of DIP (10), the pathway of DIP biosynthesis was originally proposed to occur in four steps: (i) synthesis of L-myoinositol-1-phosphate (L-I-1-P) from glucose-6-phosphate by NAD ϩ -dependent L-I-1-P synthase [inositol-1-phosphate synthase (IPS)]; (ii) hydrolysis of some of the L-I-1-P by inositol monophosphatase (IMP); (iii) coupling of the L-I-1-P with ...