PerspectiveCell Biology

Surviving Starvation

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Science  27 Jul 2001:
Vol. 293, Issue 5530, pp. 614-615
DOI: 10.1126/science.1063371

Cells engage in a delicate tightrope act: They must balance energy-efficient growth with the ability to adapt rapidly to sudden changes in their environment. For example, in an environment rich in amino acids, cells do not expend energy making enzymes required for amino acid synthesis [HN1]. However, if the environment becomes depleted of amino acids (nutritional downshift), cells will be caught lacking both the enzymes required to make amino acids and the amino acids required to make these enzymes. To solve this dilemma, cells in nutrient-poor environments must use their own proteins as sources of amino acids. Once amino acid biosynthetic enzymes start to accumulate, the cell is able to produce its own amino acids, and a new growth phase begins. On page 705 of this issue, Kuroda et al. [HN2] (1) describe the molecular components that enable cells to adapt to an environmental downshift, when a period of feast abruptly ends and leaner times roll around.

In all cells, there is increased degradation of otherwise stable proteins [HN3] during times of starvation (2). In prokaryotes, such as the bacterium Escherichia coli [HN4], starvation-induced proteolysis is an energy-dependent process requiring hydrolysis of the energy-releasing molecule adenosine triphosphate (ATP) [HN5]. The proteases [HN6] and regulatory factors responsible for protein degradation during starvation have not been identified, and little is known about which proteins are degraded. Kuroda et al. (1) present convincing evidence that protein degradation in E. coli during a nutritional downshift depends on the ATP-dependent proteases Lon and Clp [HN7]. Moreover, protein degradation in this bacterium seems to be triggered by accumulation of an unusual molecule: a string of hundreds of inorganic phosphate residues (polyphosphate) [HN8]. Finally, certain very abundant ribosomal proteins in E. coli [HN9] are the sacrificial substrates targeted for degradation during a transition from nutrient-rich to nutrient-poor conditions.

Polyphosphate accumulates in cells in response to a variety of stresses including depletion of amino acids. If the polyphosphate kinase gene (ppk) is missing and polyphosphate cannot accumulate, cells fail to recover from a shift to a nutrient-poor medium; however, addition of amino acids enables the mutant cells to resume growth [HN10] (3). Kuroda et al. show that mutations in both the Lon and Clp proteases produce the same phenotype as ppk mutations—cells fail to overcome a nutritional downshift, and addition of amino acids overcomes the block. Their biochemical analyses suggest that polyphosphate stimulates Lon protease to degrade specific proteins. Of the many cellular proteins screened as potential substrates, ribosomal proteins (not associated with intact ribosomes) were found to be preferentially targeted by the Lon-polyphosphate complex. Polyphosphate associates not only with Lon protease but also with ribosomal proteins, suggesting that it may be a specificity factor. The accumulation of polyphosphate in response to starvation and its ability to mediate degradation of substrate proteins by Lon (and possibly Clp) provides a model to explain how cells cope with a sudden depletion of the amino acid pool (see the figure).

Switching gears.

Nutrient depletion induces protein degradation. During amino acid depletion in E. coli, there is increased production of ppGpp and consequently of polyphosphate. The binding of polyphosphate to a subclass of free ribosomal proteins and to the Lon protease stimulates Lon-dependent degradation of ribosomal proteins. Amino acids are then made available to the cell by cytoplasmic peptidases that chop up the short peptides released by Lon. The cell is then able to adjust to nutrient-poor conditions by making biosynthetic enzymes from the released amino acids. In vivo, both Lon and Clp proteases appear to contribute to recovery of bacteria from a nutrient downshift.

This model provides the missing link between protein degradation and a phenomenon known as the “stringent response.” The stringent response depends on guanosine tetraphosphate (ppGpp) [HN11], a key signaling molecule in starving or nutritionally stressed cells. Synthesis of ppGpp depends on the presence of idling ribosomes and uncharged transfer RNAs [HN12] (tRNAs without their attached amino acids). This molecule integrates many of the transcriptional effects of amino acid starvation: It shuts down transcription of genes encoding ribosomal proteins and proteins involved in rapid growth, and switches on genes required for biosynthetic pathways needed to replenish depleted metabolites (4).

Intriguingly, ppGpp is also required for the accumulation of polyphosphate and for the increase in degradation of otherwise stable proteins during starvation. The Kuroda et al. work shows that these effects are all related. Polyphosphate is made by PPK and is broken down by exopolyphosphatase (PPX) [HN13]. Both enzymes are constitutively expressed, but PPX activity is inhibited by ppGpp. Consequently, when ppGpp builds up in the cell after a nutritional downshift, a decrease in PPX activity results in accumulation of polyphosphate (5). The ppGpp-dependent increase in protein degradation now can be explained by the ability of newly made polyphosphate to bind to ribosomal proteins, making them available to Lon protease for degradation (see the figure). The ribosome thus acts as a “starvation sensor,” signaling through ppGpp to the cell that it needs to tap into amino acid reserves.

How are ribosomal proteins made available for degradation? Kuroda et al. found that polyphosphate does not destabilize intact ribosomes, although they did not rule out other factors causing ribosomal disassembly during a nutritional downshift. If ribosomes are not disassembled during a downshift, then the usual regulation of ribosomal protein synthesis and assembly must be sufficiently flexible in rapidly growing cells to ensure that a store of accessible amino acids (in the form of free ribosomal proteins) is always available. Even if polyphosphate-dependent degradation is not restricted to ribosomal proteins, the increase in protein turnover during the transition phase following a nutritional downshift may be more selective than previously thought.

The adaptation of cells to a decrease in amino acid availability may differ from long-term adaptation to true starvation—in the signaling molecules used, the proteins degraded, and the proteases involved. Cells deprived of essential elements such as carbon, nitrogen, sulfur, phosphate, or metal ions, or permanently deprived of an amino acid through mutation of its biosynthetic enzyme, must enter a holding phase during which no increase in cell mass is possible. In contrast, cells undergoing a nutritional downshift need only readjust their metabolism to begin exploiting less-efficient sources of essential nutrients. It remains to be seen whether other sacrificial substrates degraded under starvation conditions are targeted by polyphosphate.

In eukaryotes, proteins to be degraded are first bound to ubiquitin [HN14], a delivery tag that targets the substrate to 26S proteasomes [HN15] or to lysosomes [HN16] for degradation. Selection of substrates for ubiquitination is under the control of a panoply of ubiquitin protein ligases, each associated with adaptor proteins. These adaptors recruit different families of proteins to the ligase depending on the presence of specific binding motifs (6). Although ubiquitin tagging is absent in prokaryotes, other adaptor proteins have evolved alternative ways to recruit specific proteins to any of five known ATP-dependent proteases. For example, phosphorylation of a response regulator that interacts with both the sigma factor RpoS and the ClpXP protease results in degradation of RpoS (7); degradation of SsrA-tagged proteins by ClpXP is accelerated by yet another adaptor, SspB (8).

Polyphosphate is particularly suitable as an adaptor during nutritional downshifts because its synthesis does not require amino acids. How does polyphosphate promote protein degradation? Perhaps the proximity of protein substrate and protease is sufficient to allow capture and degradation of the bound protein. Alternatively, the Lon protease may recognize a motif on the bound protein or some other region that becomes exposed once the protein interacts with polyphosphate.

Polyphosphate is found in all cells, including those of mammals. As it also accumulates when cells are under nonnutrient stress, its interactions with certain target proteins may turn out to be unrelated to protein degradation. The Kuroda et al. work should spur new investigations into this ubiquitous polymer and its importance in protein degradation and other stress responses.

HyperNotes Related Resources on the World Wide Web

General Hypernotes

The On-line Medical Dictionary is made available by CancerWeb.

D. Glick's Glossary of Biochemistry and Molecular Biology is provided on the Web by Portland Press.

P. Gannon's Cell & Molecular Biology Online is a collection of annotated links to Internet resources.

The CMS Molecular Biology Resource is a compendium of electronic and Internet-accessible tools and resources for molecular biology, biotechnology, molecular evolution, biochemistry, and biomolecular modeling.

The WWW Virtual Library of Cell Biology is maintained by the Fenteany Lab, Department of Chemistry, University of Illinois at Chicago.

The Google Web Directory provides links to Internet resources in biochemistry and cell biology.

The Karolinska Institutet Library, Stockholm, provides links to Internet resources on microbiology and cell biology.

The ExPASy Molecular Biology Server of the Swiss Institute of Bioinformatics provides protein-related databases and links to Internet resources.

The Companion Web Site for the third edition of Biochemistry by Mathews, van Holde, and Ahern offers definitions and introductions to concepts, molecules, and enzymes.

Webcytology is an educational Web site on unicellular biology created by students for the ThinkQuest project.

Britannica.com provides Encyclopædia Britannica articles on biochemistry, cell biology, proteins, and metabolism.

The Online Biology Book is provided by M. Farabee, Estrella Mountain Community College, Avondale, AZ.

J. Kimball offers Kimball's Biology Pages, an online biology textbook and glossary.

Cell Biology Topics are presented by G. Childs, Department of Anatomy and Neurobiology, University of Arkansas for Medical Sciences.

W. McClure, Department of Biological Sciences, Carnegie Mellon University, makes available lecture notes and other resources for a biochemistry course.

C. Rinehart, Department of Biology, Western Kentucky University, offers lecture notes for a course on molecular and cell biology.

L. Smart, Faculty of Environmental and Forest Biology, State University of New York, Syracuse, provides lecture notes for a cell physiology course.

W. Nicholson, Department of Veterinary Science and Microbiology, University of Arizona, offers lecture notes for a course on microbial physiology.

D. Smith, Division of Biology, University of California, San Diego, provides lecture notes for a course on molecular biology.

K. Todar, Department of Bacteriology, University of Wisconsin, offers lecture notes for a course on procaryotic microbiology.

A Web microbiology textbook by T. Paustian is made available by the Department of Bacteriology, University of Wisconsin.

R. Keates, Department of Chemistry and Biochemistry, University of Guelph, Canada, provides lecture notes for a course on regulation in biological systems.

M. Mulligan, Biochemistry Department, Memorial University of Newfoundland, Canada, offers lecture notes for a biochemistry course on nucleic acid biochemistry and molecular biology. A presentation titled “Protein synthesis: Folding, modification, targeting and degradation” is included.

Biochemistry (Moscow) had a special issue (vol. 63, no. 3, 2000) on inorganic polyphosphates, which included a review by T. Shiba, K. Tsutsumi, K. Ishige, and T. Noguchi titled “Inorganic polyphosphate and polyphosphate kinase: Their novel biological functions and applications” and a review by A. Kuroda and H. Ohtake titled “Molecular analysis of polyphosphate accumulation in bacteria.”

The December 1999 issue of the Journal of Biosciences of the Indian Academy of Sciences had an article by V. Velkov titled “How environmental factors regulate mutagenesis and gene transfer in microorganisms.”

Proteolytic Processing and Physiological Regulation is a 1999 colloquium proceedings available from the National Academy Press.

Numbered Hypernotes

1. The Institute of Chemistry, Freie Universität Berlin, provides a reference page on the amino acids. The Companion Web Site for Biochemistry includes an amino acid information page. The School of Crystallography, Birkbeck College, University of London, makes available an introduction to amino acids, as well as course resources on amino acids. C. Rinehart offers lecture notes on amino acids for a course on molecular and cell biology. T. Paustian's Web microbiology textbook includes a section on the synthesis of amino acids. F. Lux, Division of Biological and Physical Sciences, Lander University, Greenwood, SC, offers lecture notes on amino acid biosynthesis for a biochemistry course. L. Buehler, Division of Biology, University of California, San Diego, offers a presentation on amino acid metabolism in the lecture supplements for a course on metabolic biochemistry.

2. A. Kuroda, K. Nomura, J. Kato, T. Ikeda, N. Takiguchi, and H. Ohtake are in the Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University. R. Ohtomo and A. Kornberg are in the Department of Biochemistry, Stanford University.

3. A Protein Degradation Resource is provided by K. Wilkinson, Department of Biochemistry, Emory University School of Medicine. The Birkbank College School of Crystallography provides an introduction to protein degradation as well as a student project on protein degradation pathways prepared for a course on protein structure. J. Diwan, Department of Biology, Rensselaer Polytechnic Institute, offers lecture notes on protein degradation for a course on the biochemistry of metabolism. The Neuromuscular Disease Center Web site, provided by A. Pestronk, Washington University School of Medicine, includes a presentation on protein degradation.

4. MicroBioNet offers a presentation on E. coli. The E. coli Index, provided by G. Thomas, Department of Molecular Biology and Biotechnology, University of Sheffield, UK., provides links to Internet resources on E. coli. EcoGene, maintained by K. Rudd Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, provides information on E. coli genes and proteins. EcoCyc, available from DoubleTwist, is an encyclopedia of E. coli genes and metabolism. Colibri from the Institut Pasteur provides E. coli genomic information

5. ATP (adenosine triphosphate) is defined in the Dictionary of Science, available on the xrefer Web site. The Companion Web Site to Biochemistry includes an introduction to ATP. Britannica.com offers an Encyclopædia Britannica article on ATP; the article on metabolism has a section on the utilization of ATP. P. May, School of Chemistry, University of Bristol, UK, offers a presentation on adenosine triphosphate as a Molecule of the Month. Kimball's Biology Pages include an introduction to ATP. M. Farabee's Online Biology Book includes a section on ATP and biological energy.

6. Protease is defined in the Dictionary of Science, available on the xrefer Web site. G. Bickerstaff, Department of Biological Sciences, University of Paisley, UK, provides information on proteases in the glossary of a course on enzymology technology. The Salvesen Laboratory, Burnham Institute, La Jolla, CA, offers information on the classification and types of proteases. Prolysis, a protease and protease inhibitor Web server created by T. Moreau, Laboratory of Enzymology and Protein Chemistry, University of Tours, France, provides an introduction to the proteases.

7. Enzyme Nomenclature from the International Union of Pure and Applied Chemistry, made available on the Web by G. P. Moss, Department of Chemistry, Queen Mary and Westfield College, London, has entries for Lon and Clp. The MEROPS database, a resource on proteases maintained by the Babraham Institute, Cambridge, UK, includes entries for the Lon and Clp proteases. BRENDA, a database of enzyme information maintained by D. Schomburg's Research Group, Institute of Biochemistry, University of Cologne, Germany, includes entries for Lon (Endopeptidase La) and Clp proteases. The ExPASy Molecular Biology Server provides information about the protease Lon in the PROSITE, ENZYME, and SWISS-PROT databases; information about the protease Clp is available in the PROSITE, SWISS-PROT, and ENZYME databases. The Laboratory of Chemistry of Proteolytic Enzymes at the Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, provides a research presentation on the Lon protease. U. Jenal, Biozentrum der Universität Basel, Switzerland, discusses the Clp protease in a research presentation titled “Temporal and spatial control during the bacterial cell cycle.” The 8 June 1999 issue of the Proceedings of the National Academy of Sciences had an article by C. Smith, T. Baker, and R. Sauer titled “Lon and Clp family proteases and chaperones share homologous substrate-recognition domains”; the 20 July 1999 issue had a commentary by S. Wickner and M. Maurizi titled “Here's the hook: Similar substrate binding sites in the chaperone domains of Clp and Lon.” The 18 June 1998 issue of Current Biology had a review article by H. Feng and L. Gierasch titled “Molecular chaperones: Clamps for the Clps?”

8. The February 1995 issue of the Journal of Bacteriology had an article (full text available in Adobe Acrobat format) by A. Kornberg titled “Inorganic polyphosphate: Toward making a forgotten polymer unforgettable.” The April 1998 issue of the Journal of Bacteriology had an article by N. Rao, S. Liu, and A. Kornberg titled “Inorganic polyphosphate in Escherichia coli: The Phosphate regulon and the stringent response”; the December 2000 issue had an article by N. Ogawa, C.-M. Tzeng, C. Fraley, and A. Kornberg titled “Inorganic polyphosphate in Vibrio cholerae: Genetic, biochemical, and physiologic features.”

9. A presentation on bacterial ribosomes by J. Kahn, Department of Chemistry and Biochemistry, University of Maryland, for a biochemistry course includes a section on E. coli ribosomal proteins. I. Skerjanc, Department of Biochemistry, University of Western Ontario, provides lecture notes on ribosomes, ribosomal proteins, and polypeptide synthesis for a course on biological macromolecules.

10. Information about the ppk gene is provided in the EcoGene, EcoCyc, and Colibri databases. The 7 December 1999 issue of the Proceedings of the National Academy of Sciences had an article by A. Kuroda et al. titled “Inorganic polyphosphate kinase is required to stimulate protein degradation and for adaptation to amino acid starvation in Escherichia coli.”

11. Stringent response and guanosine tetraphosphate (ppGpp) are defined in the Companion Web Site for Biochemistry. EcoCyc illustrates the E. coli pathway of ppGpp metabolism. G. Glaser, Department of Cellular Biochemistry and Human Genetics, Faculty of Medicine, Hebrew University, Jerusalem, offers a research presentation on the stringent response in E. coli and other bacteria. D. Bryant, Department of Biochemistry and Molecular Biology, Pennsylvania State University, discusses the stringent response mechanism in lecture notes for a course on microbial physiology and structure. W. Nicholson includes a section on the stringent response in lecture notes on multigene systems and global regulation for a microbial physiology course. The Wagner Lab at the Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, offers a research presentation on ppGpp and ribosomal RNA in bacteria. The 22 August 1997 issue of the Journal of Biological Chemistry had an article by A. Kuroda, H. Murphy, M. Cashel, and A. Kornberg titled “Guanosine tetra- and pentaphosphate promote accumulation of inorganic polyphosphate in Escherichia coli“(5).

12. Transfer RNA and ribosome are defined in B. Schlindwein's Hypermedia Glossary of Genetic Terms. The Cytology Web site provided by G. Anderson, Department of Biological Sciences, University of Southern Mississippi, includes an introduction to ribosomes. Kimball's Biology Pages offer an introduction to ribosomes. G. Childs' Cell Biology Topics includes a presentation on ribosomes. The Natural Toxins Research Center at Texas A&M University makes available lecture notes by J. Pérez on the structure and function of ribosomes. L. Smart provides lecture notes on ribosomes, tRNAs, and translation for a cell physiology course. H. Luecke, Departments of Molecular Biology and Biochemistry, University of California, Irvine, provides lecture notes on tRNA and ribosomes for a biochemistry course. D. Smith offers lecture notes on tRNA and ribosomes for a molecular biology course. Scientific American makes available a 7 May 2001 Explore feature titled “Catching ribosomes in the act.”

13. EcoCyc has entries for the E. coli enzyme polyphosphate kinase (PPK) and exopolyphosphatase (PPX). The ExPASy Molecular Biology Server provides information about PPK in the ENZYME and SWISS-PROT databases; information about PPX is available in the SWISS-PROT and ENZYME databases. BRENDA has entries for PPK and PPX.

14. The Companion Web Site for Biochemistry defines ubiquitin. The Biochemistry Student Home Page at the School of Biomedical Sciences, University of Nottingham, UK, makes available a presentation titled “The ubiquitin system for protein modification and degradation.” F. Leach, Department of Biochemistry and Molecular Biology, Oklahoma State University, makes available a student review by F. Hays titled “ATP-dependent proteolysis of ubiquitinated substrates,” which was prepared for a course on metabolism and its regulation. The Neuromuscular Disease Center includes a presentation on ubiquitin-proteasome protein degradation in the section on protein degradation. R. Keates' course on regulation in biological systems includes a discussion of ubiquitin in the lecture notes on regulation of proteolysis and protein degradation. P. Petrilli, Department of Food Science, University of Naples, Italy, includes a section on ubiquitins in a presentation on proteolysis in the cell. The 28 July 2000 issue of Science had a Perspective by M. Hochstrasser titled “All in the ubiquitin family”; the 22 September 2000 issue had a Perspective by C. Joazeiro and T. Hunter titled “Ubiquitination—More than two to tango.”

15. Proteasome is defined in the Dictionary of Biology, available from xrefer. Kimball's Biology Pages include a presentation on the proteasome. T. Moreau's Prolysis Web site makes available a presentation on the architecture and structure of the proteasome. The Highlights of Biochemistry Web site, provided by R. Bergmann, Institute of General Botany, University of Hamburg, Germany, includes an illustrated presentation on proteasomes. Frontiers in Bioscience offers a 1 September 2000 review by J. A. Maupin-Furlow et al. titled “Proteasomes in the Archaea: From structure to function.”

16. Lysosome is defined in the New Penguin Dictionary of Science, available on the xrefer Web site. The Encyclopædia Britannica article on the cell has a section on the lysosome. Kimball's Biology Pages include a presentation on lysosomes. G. Childs' Cell Biology Topics includes a section on lysosomes. K. Wilkinson's Protein Degradation Resources Web site includes a presentation on lysosomal proteolysis.

17. S. Gottesman is in the Laboratory of Molecular Biology, and M. R. Maurizi is in the Laboratory of Cell Biology, of the National Cancer Institute.

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