Wednesday, October 31, 2007


Monday's Molecule was polyphosphate [Monday's Molecule #49]. Polyphosphate is a string of phosphate groups joined together by phosphoanhydride linkages. The polymer serves as a convenient storehouse for phosphorus but it also has significantt roles in regulating metabolic activity. It is present in all cells, although the specifics of its synthesis and degradation have been more intensely studied in bacteria than in eukaryotes.

One of the definitive reviews is by Arthur Kornberg et al. (1999). Here's the abstract—it pretty much describes the importance of polyphosphate.
Inorganic polyphosphate (poly P) is a chain of tens or many hundreds of phosphate (Pi) residues linked by high-energy phosphoanhydride bonds. Despite inorganic polyphosphate's ubiquity--found in every cell in nature and likely conserved from prebiotic times--this polymer has been given scant attention. Among the reasons for this neglect of poly P have been the lack of sensitive, definitive, and facile analytical methods to assess its concentration in biological sources and the consequent lack of demonstrably important physiological functions. This review focuses on recent advances made possible by the introduction of novel, enzymatically based assays. The isolation and ready availability of Escherichia coli polyphosphate kinase (PPK) that can convert poly P and ADP to ATP and of a yeast exopolyphosphatase that can hydrolyze poly P to Pi, provide highly specific, sensitive, and facile assays adaptable to a high-throughput format. Beyond the reagents afforded by the use of these enzymes, their genes, when identified, mutated, and overexpressed, have offered insights into the physiological functions of poly P. Most notably, studies in E. coli reveal large accumulations of poly P in cellular responses to deficiencies in an amino acid, Pi, or nitrogen or to the stresses of a nutrient downshift or high salt. The ppk mutant, lacking PPK and thus severely deficient in poly P, also fails to express RpoS (a sigma factor for RNA polymerase), the regulatory protein that governs > or = 50 genes responsible for stationary-phase adaptations to resist starvation, heat and oxidant stresses, UV irradiation, etc. Most dramatically, ppk mutants die after only a few days in stationary phase. The high degree of homology of the PPK sequence in many bacteria, including some of the major pathogenic species (e.g. Mycobacterium tuberculosis, Neisseria meningitidis, Helicobacter pylori, Vibrio cholerae, Salmonella typhimurium, Shigella flexneri, Pseudomonas aeruginosa, Bordetella pertussis, and Yersinia pestis), has prompted the knockout of their ppk gene to determine the dependence of virulence on poly P and the potential of PPK as a target for antimicrobial drugs. In yeast and mammalian cells, exo- and endopolyphosphatases have been identified and isolated, but little is known about the synthesis of poly P or its physiologic functions. Whether microbe or human, all species depend on adaptations in the stationary phase, which is truly a dynamic phase of life. Most research is focused on the early and reproductive phases of organisms, which are rather brief intervals of rapid growth. More attention needs to be given to the extensive period of maturity. Survival of microbial species depends on being able to manage in the stationary phase. In view of the universality and complexity of basic biochemical mechanisms, it would be surprising if some of the variety of poly P functions observed in microorganisms did not apply to aspects of human growth and development, to aging, and to the aberrations of disease. Of theoretical interest regarding poly P is its antiquity in prebiotic evolution, which along with its high energy and phosphate content, make it a plausible precursor to RNA, DNA, and proteins. Practical interest in poly P includes many industrial applications, among which is the microbial removal of Pi in aquatic environments.
Much work has been done since this review was published in 1999 but the basic concepts haven't changed. Arthur Kornberg [Biochemist Arthur Kornberg (1918 - 2007)] was very interested in polyphosphates and he is responsible bringing it to the attention of the biochemistry community. His lab worked on polyphosphates for the past 25 years. As you know, Kornberg died last Friday but one of his papers on polyphosphate was just published two weeks ago (Zhang et al. 2007). That paper describes the enzyme polyphosphate kinase 1 in slime mold Dictyostelium discoideum, one of the few eukaryotes to have the enzyme that makes and degrades polyphosphate. The paper shows that polyphosphate regulates cell division in Dictyostelium.

In a paper published earlier this year Kornberg's lab showed that E. coli ppk mutant cells do not support lytic infection by bacteriophage P1 (Li et al. 2007). The mutant cells lack polyphosphate. P1 growth is inhibited because the transcriptional activator for late gene synthesis is not activate in the absence of polyphophate.

Kornberg, A., Rao, N.N. and Ault-Riché, D. (1999) Inorganic polyphosphate: a molecule of many functions. Annu. Rev. Biochem. 68:89-125. [PubMed]

Li, L., Rao, N.N. and Kornberg, A. (2007) Inorganic polyphosphate essential for lytic growth of phages P1 and fd. Proc. Natl. Acad. Sci. (USA) 104(6):1794-1799. [PubMed]

Zhang, H., Gómez-García, M.R., Shi, X., Rao, N.N. and Kornberg, A. (2007) Polyphosphate kinase 1, a conserved bacterial enzyme, in a eukaryote, Dictyostelium discoideum, with a role in cytokinesis. Proc. Natl. Acad. Sci. (USA) 104:16486-16491. [PNAS] [PubMed]


  1. Maybe only tangentially related to this, but there was a paper from Solomon Snyder in PNAS a little while back where he suggested that protein phosphorylation may often in fact be pyrophosphorylation, and that this is mediated by the pyrophosphorylated inositols IP7 and IP8. This seems pretty important, and surprising if it had been missed all these years

  2. This stuff is highly relevant to the origin of life also. Polyphosphate can be produced geologically by heating certain rocks, and provides chemical energy very similar to ATP, GTP etc.

  3. Nick, assuming that the natural formation of polyphosphate from inorganic phosphate was at equilibrium in the primordial soup, it follows that the Gibbs free energy change will be zero for the hydrolysis of pyrophosphate.

    The only way that naturally occurring pyrophosphate could be a significant source of chemical energy would be if it's concentration was a lot higher than the equilibrium value. How do you envisage that this could happen in the warm little pond where life began? How long would that situation last if primitive life started using pyrophosphate as a source of chemical energy? Minutes? Hours? Days?