Inorganic Polyphosphates

by Schroder, Heinz Christoph; Muller, Werner E. G.

• ISBN13: 9783540653035
• ISBN10: 3540653031
• Format: Hardcover
• Copyright: 1999-07-01
• Publisher: Springer Verlag

Summary

Inorganic polyphosphates - polymers of orthophosphate linked by high-energy phosphoanhydride bonds - have been found in apparently all forms of life, from bacteria, yeasts & fungi to higher plants & animals. These polymers, which had been neglected for a long time, have become a fascinating area of research in the last few years. This volume summarizes the present state of knowledge about the metabolism & function of inorganic polyphosphates. In addition, the methods to study these polymers as well as the biotechnological applications of inorganic polyphosphates are described. The 15 chapters of this volume, dealing with different aspects of polyphosphate research, are written by experts in the field. This book represents a valuable source of information not only for researchers working on this subject, but also for scientists interested in fundamental aspects of cell & energy metabolism.

Table of Contents

Inorganic Polyphosphate: A Molecule of Many Functions
A. Kornberg
Introduction	1	(1)
Metachromatic Granules Are Inorganic PolyP	2	(1)
Occurrence and Enzymology of PolyP	2	(3)
Biosynthesis of PolyP	5	(3)
Functions of PolyP	8	(3)
ATP Substitute and Energy Source	8	(1)
A Reservoir for Pi	9	(1)
Chelator of Metal Ions	9	(1)
Buffer Against Alkali	9	(1)
Channel for DNA Entry	10	(1)
Regulator for Stress and Survival	10	(1)
Regulator of Development	11	(1)
Cell Capsule	11	(1)
PolyP in Animal Cells and Tissues	11	(1)
Prebiotic Role of PolyP	12	(1)
Industrial Applications of PolyP	13	(2)
Depollution of Pi in the Environment	13	(1)
Antibacterial Action	13	(1)
PolyP Kinase as an Antimicrobial Target	13	(1)
Source of ATP (NTPs)	14	(1)
Insulating Fibers	15	(1)
Summary	15	(4)
References	16	(3)
Research in Inorganic Polyphosphates: The Beginning
P. Langen
From the Last Decade of the Previous Century to the Middle of the Present One: The Discovery of Polyphosphates in Yeast and Other Microorganisms and the Elucidation of Their Structure	19	(2)
Polyphosphate Synthesis. How and Where Does it Start?	21	(6)
References	24	(3)
Metabolism and Function of Polyphosphates in Bacteria and Yeast
I.S. Kulaev
T.V. Kulakovskaya
N.A. Andreeva
L.P. Lichko
Introduction	27	(1)
Polyphosphates and Enzymes of Their Metabolism in Prokaryotes	27	(3)
Polyphosphates and Enzymes of Their Metabolism in Lower Eukaryotes	30	(3)
Exopolyphosphatases of Yeast Cells: Compartmentation and Properties	33	(12)
References	40	(5)
Inorganic Polyphosphate in Eukaryotes: Enzymes, Metabolism and Function
H.C. Schroder
B. Lorenz
L. Kurz
W.E.G. Muller
Introduction	45	(1)
Occurrence of PolyP in Eukaryotic Cells	45	(4)
Variations in Cellular PolyP Content	48	(1)
Subcellular Localization	49	(1)
PolyP-Dependent Enzymes	49	(11)
PolyP Synthesis: Polyphosphate Kinase	50	(1)
PolyP Degradation: Polyphosphatases	51	(1)
Exopolyphosphatases	52	(6)
Endopolyphosphatases	58	(1)
Further PolyP-Dependent Enzymes	59	(1)
PolyP-Binding Proteins	60	(1)
Biological Functions of PolyP	60	(7)
Energy Source	61	(1)
Phosphate Reserve and Phosphate Donor for Kinases	61	(1)
Regulator of Cellular Enzymes	62	(1)
Regulator of Levels of Intracellular Adenylate Nucleotides	62	(1)
Regulator of DNA-Histone Interaction and Other Functions in the Cell Nucleus	63	(1)
Formation of Calcium Channels Across Membranes	64	(1)
Chelator for Divalent Cations and Counterion for Basic Molecules	65	(1)
Regulator of Cellular Stress Response	66	(1)
Antibacterial and Antiviral Agent	67	(1)
PolyP Metabolism During Ageing and Development	67	(2)
Changes in PolyP Metabolism During Apoptosis	69	(1)
PolyP in Human Bone Formation	70	(2)
PolyP and Disease	72	(2)
Concluding Remarks	74	(9)
References	74	(9)
Cyclic Condensed Metaphosphates in Plants and the Possible Correlations Between Inorganic Polyphosphates and Other Compounds
R. Niemeyer
Nomenclature and Structure of Inorganic Condensed Phosphates	83	(1)
Linear Condensed Polyphosphates	83	(1)
Cyclic Condensed Metaphosphates	84	(1)
Ultraphosphates	84	(1)
Extraction Methods of Condensed Inorganic Phosphates	84	(3)
Hydrolysis Free Extraction Method as a Prerequisite for Metabolic Investigation	84	(1)
Hydrolysis Free Extraction, Separation and Identification of Metaphosphates Together with Inositol Phosphates and Nucleic Acids	85	(2)
Radioactivity Pattern of Condensed Phosphates and Inositol Phosphates After Fractionation on Slab Gels	87	(5)
Quantitative Distribution of Incorporated 32P-Orthophosphate in Six Different Fractions	92	(2)
The Metabolic Model of Condensed Phosphates	94	(7)
References	98	(3)
Polyphosphate Glucokinase
N.F.B. Phillips
P.C. Hsieh
T.H. Kowalczyk
Introduction	101	(1)
An Historical Perspective	102	(1)
Involvement of PolyP Glucokinase in Metabolism	102	(1)
Multiple Forms of PolyP Glucokinase and Molecular Weight Characterization	103	(1)
Bifunctionality	104	(1)
PolyP and ATP Glucokinase Activities Are Catalyzed by a Single Enzyme	105	(1)
PolyP and ATP Have Separate Binding Sites	105	(1)
The Glucose-Phosphorylating Center Is Common for Both PolyP and ATP	106	(3)
Kinetic Evidence	106	(1)
Substrate Competition	106	(1)
Affinity Labeling with Nucleotide Analogs	107	(1)
Structural Evidence	107	(2)
Mechanism of the PolyP Glucokinase Reaction	109	(5)
Mechanism of the Mycobacterial Enzyme	109	(1)
Kinetic Mechanism of the PolyP-Dependent Reaction	109	(1)
Kinetic Mechanism of the ATP-Dependent Reaction	109	(1)
Kinetic Mechanism of the P. shermanii Enzyme	110	(1)
Mechanism of PolyP Utilization: Processivity vs Nonprocessivity	110	(2)
Preferntial Utilization of Long Chains Over Short Chains Is Due to Better Binding Affinities Rather than Faster Catalysis or Product Release	112	(2)
Influence of Glycerol on Kinetic Parameters	114	(1)
Which Reaction Is Favorable in M. tuberculosis?	114	(1)
Cloning and Expression of the PolyP Glucokinase Gene from M. tuberculosis	115	(1)
Characterization of the PolyP Glucokinase Gene	116	(1)
Identification of Substrate Binding Domains of PolyP Glucokinase and Other ATP Hexokinases	116	(1)
Proposed Substrate-Binding Domains of PolyP Glucokinase	117	(2)
The ATP-Binding Site	117	(1)
The Adenosine Site	117	(1)
The Glucose-Binding Site	118	(1)
The PolyP-Binding Site	119	(1)
Evolutionary Significance of PolyP Glucokinase	119	(2)
Transition from PolyP to ATP as the Phosphoryl Donor in Glucose Phosphorylation	119	(1)
Bifunctional PolyP Glucokinase May be an ``Intermediate'' in the Evolution of Hexokinases and Glucokinases	120	(1)
Concluding Remarks	121	(6)
References	122	(5)
Cytoplasmic Inorganic Pyrophosphatase
A.A. Baykov
B.S. Coorperman
A. Goldman
R. Lahti
Introduction	127	(1)
Catalytic Properties	128	(2)
Substrate and Metal Activator Specificity	128	(1)
Pyrophosphate Synthesis	129	(1)
Oxygen Exchange	129	(1)
Inhibitors	130	(1)
Pyrophosphatase Gene	130	(4)
Cloning the Gene	130	(1)
Expressing the Genes and Producing Enzyme Variants	131	(1)
Conservation of Enzyme Primary Structure	131	(3)
Three-Dimensional Structure	134	(6)
Monomeric Structure	135	(1)
Active Site Structure	136	(2)
Oligomeric Structure	138	(1)
The Role of Oligomeric Structure in Catalysis and Thermostability	139	(1)
Mechanism of Catalysis of Water Attack on PPi	140	(11)
Assignment of P1 and P2	142	(1)
Consistency with Model Studies	142	(1)
The General Acid	143	(1)
The Nucleophilic Water	143	(1)
Relaxation at the Active Site: Alternative Mechanisms	144	(1)
References	145	(6)
Polyphosphate/Poly-(R)-3-hydroxybutyrate Ion Channels in Cell Membranes
R.N. Reusch
Introduction	151	(1)
Inorganic Polyphosphates: Cation Attraction, Selection, and Transport	152	(1)
Poly-(R)-3-Hydroxybutyrate)	153	(9)
Low Molecular Weight Poly-(R)-3-Hydroxybutyrate in Bacterial Membranes	154	(4)
Poly-(R)-3-Hydroxybutyrate as an Amphiphilic Salt Solvent	158	(2)
Poly-(R)-3-Hydroxybutyrate Ion Channels in Planar Lipid Bilayers	160	(2)
Polyphosphate/Poly-(R)-3-Hydroxybutyrate Complexes in Bacterial Membranes	162	(4)
Selectivity for Calcium	162	(1)
Models for the Structure of PolyP/Poly-(R)-3-Hydroxybutyrate Membrane Complexes	163	(3)
Polyphosphate/Poly-(R)-3-Hydroxybutyrate Complexes in Planar Lipid Bilayers	166	(7)
E. Coli PolyP/Poly-(R)-3-Hydroxybutyrate Complexes as Ion Channels	166	(3)
Completely Synthetic PolyP/Poly-(R)-3-Hydroxybutyrate Complexes as Ion Channels	169	(1)
Cation Selectivity of PolyP/Poly-(R)-3-Hydroxybutyrate Channels	170	(1)
Blockage of PolyP/Poly-(R)-3-Hydroxybutyrate Channels	171	(1)
How Do PolyP/Poly-(R)-3-Hydroxybutyrate Channels Work?	172	(1)
Polyphosphate/Poly-(R)-3-Hydroxybutyrate Complexes as Calcium Pumps	173	(2)
Polyphosphate/Poly-(R)-3-Hydroxybutyrate Complexes as DNA Channels?	175	(2)
Evolutionary Aspects and Concluding Remarks	177	(6)
References	178	(5)
Inorganic Polyphosphate Regulates Responses of Escherichia coli to Nutritional Stringencies, Environmental Stresses and Survival in the Stationary Phase
N.N. Rao
A. Kornberg
Introduction	183	(1)
Nutritional Stringencies and Environmental Stress	183	(4)
Phosphate Limitation: phoB and pho Regulon	184	(1)
Amino Acid and Phosphate Limitation	185	(1)
(p)ppGpp and in Vivo Synthesis of PolyP	185	(1)
Accumulation of PolyP is Due to Inhibition of Exopolyphosphatase by (p)ppGpp	186	(1)
Nitrogen Starvation: rpoN	186	(1)
Nutritional Shift from Rich to Minimal Medium and the Reverse	186	(1)
Osmotic Stress	186	(1)
Stationary Phase Adaptations	187	(2)
Heat Sensitivity	187	(1)
Response to Oxidative Stress and Sensitivity to Menadione	187	(1)
Sensitivity to UV and Osmotic Challenge	188	(1)
HPII Expression	189	(1)
Reduced Survival and Growth Defects	189	(1)
PolyP and Induction of rpoS Expression	189	(2)
Transcription of katE is not Induced in Cells Lacking PolyP	190	(1)
Transcription of rpoS Gene	190	(1)
Cellular Levels of RpoS in PolyP-Minus Cells	191	(1)
PolyP-Binding Proteins and Metal Complexes	191	(1)
PolyP-Binding Proteins	191	(1)
Heavy Metals and Polyamines	191	(1)
Metal-PolyP Complexes and Membrane Potential	192	(1)
Summary	192	(5)
References	193	(4)
From Polyphosphates to Bisphosphonates and Their Role in Bone and Calcium Metabolism
H.Fleisch
Introduction	197	(1)
Pyrophosphates and Polyphosphates	197	(3)
Bisphosphonates	200	(10)
Chemistry	200	(1)
Physicochemical Effects	200	(1)
Biological Effects	201	(1)
Inhibition of Bone Resorption	201	(7)
Inhibition of Calcification	208	(1)
Pharmacokinetics	209	(1)
Discussion	210	(1)
Further Information	210	(7)
References	210	(7)
Methods for Investigation of Inorganic Polyphosphates and Polyphosphate-Metabolizing Enzymes
B. Lorenz
H.C. Schroder
Introduction	217	(1)
Preparation of Inorganic Polyphosphates	217	(4)
Chemical Synthesis	217	(2)
Radiolabeled Polyphosphates	219	(1)
Enzymatic Synthesis	220	(1)
Synthesis by Living Cells or Organisms	220	(1)
Isolation of Polyphosphates from Cells and Tissues	221	(2)
Isolation Procedures	221	(2)
Analysis of Polyphosphates and Measuring of Enzyme Activities	223	(7)
Basic Dyes	224	(1)
Determination of Orthophosphate Using Ammonium Molybdate	224	(1)
Radioassays	225	(1)
Fura-2 Method	226	(1)
Enzymatic Assays	227	(3)
Detection of Polyphosphates in Whole Cells and Tissues	230	(1)
Separation of Polyphosphates and Determination of Their Chain Lengths	230	(11)
Thin-Layer Chromatography	231	(1)
Ion-Exchange Chromatography	231	(1)
High-Performance Liquid Chromatography	231	(2)
Gel Electrophoresis	233	(1)
Gel Filtration	234	(1)
Other Methods for Determination of Chain Lengths	235	(1)
References	236	(5)
Definitive Enzymatic Assays in Polyphosphate Analysis
D. Ault-Riche
A. Kornberg
Introduction	241	(1)
Enzymes Used in Assays of PolyP	242	(3)
PolyP Kinase (PPK)	242	(1)
Exopolyphosphatase (PPX)	243	(1)
Other Enzymes	244	(1)
Purification and Assay of Recombinant PPK	245	(1)
Purification and Assay of Recombinant PPX	246	(1)
Rapid Preparation of 32P-PolyP	247	(1)
Estimating PolyP in Biological Samples	248	(2)
Radioactive Assay of PolyP with PPX	248	(1)
Non-radioactive Assay of PolyP with PPK	249	(1)
High Throughput (HTP) Assay of PolyP	249	(1)
Future Directions in Assay Development	250	(3)
References	251	(2)
Study of Polyphosphate Metabolism in Intact Cells by 31-P Nuclear Magnetic Resonance Spectroscopy
K.Y. Chen
Introduction	253	(1)
Phosphorus NMR	254	(2)
Basic Principles of NMR	254	(1)
Phosphorus NMR	255	(1)
Polyphosphates	256	(1)
Inorganic and Organic	256	(1)
Metabolism, Regulation, and Function	256	(1)
Use of Phosphorus NMR to Study Polyphosphate in Intact Cells	257	(13)
NMR Apparatus and Sample Preparations	257	(2)
Specific Information Gained on PolyP from Phosphorus NMR	259	(1)
Eubacteria	260	(1)
Escherichia coli	260	(1)
Propionibacterium acnes	261	(2)
Acinetobacter johnsonii	263	(1)
Lower Eukaryotes	263	(1)
Yeast	263	(3)
Neurospora crassa	266	(2)
Physarum polycephalum	268	(1)
Aspergillus terreus	269	(1)
Algae	269	(1)
Plant and Animal Cells	270	(1)
Conclusions	270	(5)
References	271	(4)
Polyphosphate-Accumulating Bacteria and Enhanced Biological Phosphorus Removal
G.J.J. Kortstee
H.W. van Veen
Introduction	275	(1)
Chemistry of Inorganic Condensed Phosphates	276	(1)
Functions of PolyP in Bacteria	277	(4)
Energy Source	277	(2)
Acquisition of Competence	279	(1)
Uptake of Ca2+	280	(1)
Biosynthesis and Biodegradation of PolyP in Acinetobacter spp	281	(4)
Biosynthesis	281	(2)
Biodegradation	283	(2)
Phosphate Transport in Acinetobacter johnsonii 210A	285	(3)
Uptake and Efflux	285	(2)
Pi Efflux as an Energy-Recycling Mechanism	287	(1)
Enhanced Biological Phosphorus Removal (EBPR)	288	(5)
The Process	288	(2)
The Biochemical Model	290	(2)
The Bacteria Involved	292	(1)
Conclusions and Outlook	293	(6)
References	294	(5)
Genetic Improvement of Bacteria for Enhanced Biological Removal of Phosphate from Wastewater
H. Ohtake
A. Kuroda
J. Kato
T. Ikeda
Introduction	299	(1)
Strategy of Genetic Improvement of Escherichia coli	300	(1)
Rate-Limiting Step for PolyP Accumulation	301	(3)
PolyP Accumulation Capacity	304	(2)
PolyP Accumulation in Klebsiella aerogenes	306	(3)
Concluding Remarks	309	(4)
References	309	(4)
Subject Index	313