A pyrophosphate-dependent phosphofructokinase (PP i -PFK) and an ATP-dependent phosphofructokinase (ATP-PFK) from Thermotoga maritima have been cloned and characterized. The PP i -PFK is unique in that the K m and V max values indicate that polyphosphate is the preferred substrate over pyrophosphate; the enzyme in reality is a polyphosphate-dependent PFK. The ATP-PFK was not significantly affected by common allosteric effectors (e.g., phosphoenolpyruvate) but was strongly inhibited by PP i and polyphosphate. The results suggest that the control of the Embden-Meyerhof pathway in this organism is likely to be modulated by pyrophosphate and/or polyphosphate.The Embden-Meyerhof (EM), or glycolytic, pathway is nearly ubiquitous in all life forms, and enzymes of the reaction sequence are highly conserved. One of the key and definitive enzymes of the pathway is phosphofructokinase (PFK). In the majority of organisms, ATP is the phosphoryl donor for the enzyme and the reaction is a nonreversible step in the pathway. Due to its position, PFK is usually allosterically regulated by intracellular metabolites, e.g., phosphoenolpyruvate (PEP), GDP, and/or ADP (27). PFK subtypes utilizing pyrophosphate (PP i ) as the phosphoryl donor, where the reaction becomes more reversible and the enzyme is generally not subject to allosteric control mechanisms, have also been described (16,18,25).Thermotoga maritima is a non-spore-forming, rod-shaped hyperthermophilic bacterium with an optimum growth temperature of 80°C and is phylogenetically classified in the order Thermotogales. The phylogeny of the small-subunit rRNA shows that this organism represents one of the deepest and most slowly evolving lineages of bacteria (12). T. maritima ferments various carbohydrates, including monosaccharides and polysaccharides, primarily via the EM pathway, and ATPdependent PFK (ATP-PFK) activity in cell extracts has been reported (23, 24). The genome sequence of this organism indicated the presence of another PFK gene, and sequence comparison showed homology to PP i -dependent PFK (PP i -PFK) enzymes (17). If both genes code for functional enzymes, then Thermotoga would represent the unusual situation of an organism possessing two distinct PFK activities. Because of its phylogenetic position, the occurrence and origin of these genes are of importance with respect to the origins of the EM pathway. This paper describes the cloning, expression, and characterization of these enzymes, both of which exhibit unusual features.T. maritima strain 3109 was obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH and grown in the medium described by Huber et al. (12). Escherichia coli DH5␣ and expression plasmid pPROEX HTb were obtained from Life Technologies. E. coli was grown at 30°C with vigorous aeration (200 rpm) in Luria-Bertani broth supplemented with ampicillin (100 g ml Ϫ1 ) when appropriate. The PFK assay was conducted essentially as described by Ding et al. (6). Preparation of genomic DNA and the alkaline lysis and cesium chlorid...