1
|
Ahmad S, Gordon IJ, Tsang KK, Alexei AG, Sychantha D, Colautti J, Trilesky SL, Kim Y, Wang B, Whitney JC. Identification of a broadly conserved family of enzymes that hydrolyze (p)ppApp. Proc Natl Acad Sci U S A 2023; 120:e2213771120. [PMID: 36989297 PMCID: PMC10083569 DOI: 10.1073/pnas.2213771120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 02/25/2023] [Indexed: 03/30/2023] Open
Abstract
Bacteria produce a variety of nucleotide second messengers to adapt to their surroundings. Although chemically similar, the nucleotides guanosine penta- and tetraphosphate [(p)ppGpp] and adenosine penta- and tetraphosphate [(p)ppApp] have distinct functions in bacteria. (p)ppGpp mediates survival under nutrient-limiting conditions and its intracellular levels are regulated by synthetases and hydrolases belonging to the RelA-SpoT homolog (RSH) family of enzymes. By contrast, (p)ppApp is not known to be involved in nutrient stress responses and is synthesized by RSH-resembling toxins that inhibit the growth of bacterial cells. However, it remains unclear whether there exists a family of hydrolases that specifically act on (p)ppApp to reverse its toxic effects. Here, we present the structure and biochemical characterization of adenosine 3'-pyrophosphohydrolase 1 (Aph1), the founding member of a monofunctional (p)ppApp hydrolase family of enzymes. Our work reveals that Aph1 adopts a histidine-aspartate (HD)-domain fold characteristic of phosphohydrolase metalloenzymes and its activity mitigates the growth inhibitory effects of (p)ppApp-synthesizing toxins. Using an informatic approach, we identify over 2,000 putative (p)ppApp hydrolases that are widely distributed across bacterial phyla and found in diverse genomic contexts, and we demonstrate that 12 representative members hydrolyze ppApp. In addition, our in silico analyses reveal a unique molecular signature that is specific to (p)ppApp hydrolases, and we show that mutation of two residues within this signature broadens the specificity of Aph1 to promiscuously hydrolyze (p)ppGpp in vitro. Overall, our findings indicate that like (p)ppGpp hydrolases, (p)ppApp hydrolases are widespread in bacteria and may play important and underappreciated role(s) in bacterial physiology.
Collapse
Affiliation(s)
- Shehryar Ahmad
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ONL8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ONL8S 4K1, Canada
| | - Isis J. Gordon
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX75235
| | - Kara K. Tsang
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Andrea G. Alexei
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ONL8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ONL8S 4K1, Canada
| | - David Sychantha
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ONL8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ONL8S 4K1, Canada
| | - Jake Colautti
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ONL8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ONL8S 4K1, Canada
| | - Sarah L. Trilesky
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ONL8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ONL8S 4K1, Canada
| | - Youngchang Kim
- Structural Biology Center, X-ray Science, Argonne National Laboratory, Argonne, IL60439
| | - Boyuan Wang
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - John C. Whitney
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ONL8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ONL8S 4K1, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ONL8S 4K1, Canada
| |
Collapse
|
2
|
Potrykus K, Thomas NE, Bruhn-Olszewska B, Sobala M, Dylewski M, James T, Cashel M. Estimates of Rel Seq, Mesh1, and SAH Mex Hydrolysis of (p)ppGpp and (p)ppApp by Thin Layer Chromatography and NADP/NADH Coupled Assays. Front Microbiol 2020; 11:581271. [PMID: 33193211 PMCID: PMC7644958 DOI: 10.3389/fmicb.2020.581271] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022] Open
Abstract
The Mesh1 class of hydrolases found in bacteria, metazoans and humans was discovered as able to cleave an intact pyrophosphate residue esterified on the 3'hydroxyl of (p)ppGpp in a Mn2+ dependent reaction. Here, thin layer chromatography (TLC) qualitative evidence is presented indicating the substrate specificity of Mesh1 from Drosophila melanogaster and human MESH1 also extends to the (p)ppApp purine analogs. More importantly, we developed real time enzymatic assays, coupling ppNpp hydrolysis to NADH oxidation and pppNpp hydrolysis to NADP+ reduction, which facilitate estimation of kinetic constants. Furthermore, by using this assay technique we confirmed TLC observations and also revealed that purified small alarmone hydrolase (SAHMex) from Methylobacterium extorquens displays a strong hydrolase activity toward (p)ppApp but only negligible activity toward (p)ppGpp. In contrast, the substrate specificity of the hydrolase present in catalytically active N-terminal domain of the RSH protein from Streptococcus equisimilis (RelSeq) includes (p)ppGpp but not (p)ppApp. It is noteworthy that the RSH protein from M. extorquens (RSHMex) has been recently shown to synthesize both (p)ppApp and (p)ppGpp.
Collapse
Affiliation(s)
- Katarzyna Potrykus
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Nathan E Thomas
- Intramural Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Bożena Bruhn-Olszewska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Michał Sobala
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Maciej Dylewski
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Tamara James
- Intramural Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Michael Cashel
- Intramural Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
3
|
Steinchen W, Zegarra V, Bange G. (p)ppGpp: Magic Modulators of Bacterial Physiology and Metabolism. Front Microbiol 2020; 11:2072. [PMID: 33013756 PMCID: PMC7504894 DOI: 10.3389/fmicb.2020.02072] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/06/2020] [Indexed: 01/21/2023] Open
Abstract
When bacteria experience growth-limiting environmental conditions, the synthesis of the hyperphosphorylated guanosine derivatives (p)ppGpp is induced by enzymes of the RelA/SpoT homology (RSH)-type protein family. High levels of (p)ppGpp induce a process called "stringent response", a major cellular reprogramming during which ribosomal RNA (rRNA) and transfer RNA (tRNA) synthesis is downregulated, stress-related genes upregulated, messenger RNA (mRNA) stability and translation altered, and allocation of scarce resources optimized. The (p)ppGpp-mediated stringent response is thus often regarded as an all-or-nothing paradigm induced by stress. Over the past decades, several binding partners of (p)ppGpp have been uncovered displaying dissociation constants from below one micromolar to more than one millimolar and thus coincide with the accepted intracellular concentrations of (p)ppGpp under non-stringent (basal levels) and stringent conditions. This suggests that the ability of (p)ppGpp to modulate target proteins or processes would be better characterized as an unceasing continuum over a concentration range instead of being an abrupt switch of biochemical processes under specific conditions. We analyzed the reported binding affinities of (p)ppGpp targets and depicted a scheme for prioritization of modulation by (p)ppGpp. In this ranking, many enzymes of e.g., nucleotide metabolism are among the first targets to be affected by rising (p)ppGpp while more fundamental processes such as DNA replication are among the last. This preference should be part of (p)ppGpp's "magic" in the adaptation of microorganisms while still maintaining their potential for outgrowth once a stressful condition is overcome.
Collapse
Affiliation(s)
- Wieland Steinchen
- Department of Chemistry, Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | | | - Gert Bange
- Department of Chemistry, Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| |
Collapse
|
4
|
Haas TM, Qiu D, Häner M, Angebauer L, Ripp A, Singh J, Koch HG, Jessen-Trefzer C, Jessen HJ. Four Phosphates at One Blow: Access to Pentaphosphorylated Magic Spot Nucleotides and Their Analysis by Capillary Electrophoresis. J Org Chem 2020; 85:14496-14506. [PMID: 32502348 PMCID: PMC7684580 DOI: 10.1021/acs.joc.0c00841] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
complex phosphorylation pattern of natural and modified pentaphosphorylated
magic spot nucleotides is generated in a highly efficient way. A cyclic
pyrophosphoryl phosphoramidite (cPyPA) reagent is used to introduce
four phosphates on nucleosides regioselectively in a one-flask key
transformation. The obtained magic spot nucleotides are used to develop
a capillary electrophoresis UV detection method, enabling nucleotide
assignment in complex bacterial extracts.
Collapse
Affiliation(s)
- Thomas M Haas
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Danye Qiu
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Markus Häner
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Larissa Angebauer
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Alexander Ripp
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Jyoti Singh
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Claudia Jessen-Trefzer
- Institute of Pharmaceutical Biology and Biotechnology, University of Freiburg, 79104 Freiburg, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany.,CIBSS, Centre for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
5
|
A widespread toxin-antitoxin system exploiting growth control via alarmone signaling. Proc Natl Acad Sci U S A 2020; 117:10500-10510. [PMID: 32345719 PMCID: PMC7229694 DOI: 10.1073/pnas.1916617117] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The alarmone (p)ppGpp is a central signaling nucleotide that is synthesized by RelA-SpoT Homologue (RSH) enzymes, and rewires bacterial physiology in response to stress. It is an unanswered question why bacteria often carry multiple (p)ppGpp-synthesising RSHs in the same genome. We have answered that question for five subfamilies of small alarmone synthetases (SASs) by discovering that they are toxins of a novel toxin−antitoxin system, and that they act by synthesizing ppGpp and its unusual analogue—ppApp. These distinct toxic SAS (toxSAS) subfamilies are neutralized by six neighboring antitoxin genes. The toxSAS system and its weaponizing of nucleotide second messengers gives a new angle to the hotly debated and controversial topic of cross-talk between TAs and the alarmone-mediated stringent response. Under stressful conditions, bacterial RelA-SpoT Homolog (RSH) enzymes synthesize the alarmone (p)ppGpp, a nucleotide second messenger. (p)ppGpp rewires bacterial transcription and metabolism to cope with stress, and, at high concentrations, inhibits the process of protein synthesis and bacterial growth to save and redirect resources until conditions improve. Single-domain small alarmone synthetases (SASs) are RSH family members that contain the (p)ppGpp synthesis (SYNTH) domain, but lack the hydrolysis (HD) domain and regulatory C-terminal domains of the long RSHs such as Rel, RelA, and SpoT. We asked whether analysis of the genomic context of SASs can indicate possible functional roles. Indeed, multiple SAS subfamilies are encoded in widespread conserved bicistronic operon architectures that are reminiscent of those typically seen in toxin−antitoxin (TA) operons. We have validated five of these SASs as being toxic (toxSASs), with neutralization by the protein products of six neighboring antitoxin genes. The toxicity of Cellulomonas marina toxSAS FaRel is mediated by the accumulation of alarmones ppGpp and ppApp, and an associated depletion of cellular guanosine triphosphate and adenosine triphosphate pools, and is counteracted by its HD domain-containing antitoxin. Thus, the ToxSAS–antiToxSAS system with its multiple different antitoxins exemplifies how ancient nucleotide-based signaling mechanisms can be repurposed as TA modules during evolution, potentially multiple times independently.
Collapse
|
6
|
Sobala M, Bruhn-Olszewska B, Cashel M, Potrykus K. Methylobacterium extorquens RSH Enzyme Synthesizes (p)ppGpp and pppApp in vitro and in vivo, and Leads to Discovery of pppApp Synthesis in Escherichia coli. Front Microbiol 2019; 10:859. [PMID: 31068922 PMCID: PMC6491832 DOI: 10.3389/fmicb.2019.00859] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/03/2019] [Indexed: 01/12/2023] Open
Abstract
In bacteria, the so-called stringent response is responsible for adaptation to changing environmental conditions. This response is mediated by guanosine derivatives [(p)ppGpp], synthesized by either large mono-functional RelA or bi-functional SpoT (synthesis and hydrolysis) enzymes in β- and γ-proteobacteria, such as Escherichia coli. In Firmicutes and α-, δ-, and 𝜀-proteobacteria, large bifunctional Rel-SpoT-homologs (RSH), often accompanied by small (p)ppGpp synthetases and/or hydrolases devoid of regulatory domains, are responsible for (p)ppGpp turnover. Here, we report on surprising in vitro and in vivo properties of an RSH enzyme from Methylobacterium extorquens (RSHMex). We find that this enzyme possesses some unique features, e.g., it requires cobalt cations for the most efficient (p)ppGpp synthesis, in contrast to all other known specific (p)ppGpp synthetases that require Mg2+. In addition, it can synthesize pppApp, which has not been demonstrated in vitro for any Rel/SpoT/RSH enzyme so far. In vivo, our studies also show that RSHMex is active in Escherichia coli cells, as it can complement E. coli ppGpp0 growth defects and affects rrnB P1-lacZ fusion activity in a way expected for an RSH enzyme. These studies also led us to discover pppApp synthesis in wild type E. coli cells (not carrying the RSHMex enzyme), which to our knowledge has not been demonstrated ever before. In the light of our recent discovery that pppApp directly regulates E. coli RNAP transcription in vitro in a manner opposite to (p)ppGpp, this leads to a possibility that pppApp is a new member of the nucleotide second-messenger family that is widely present in bacterial species.
Collapse
Affiliation(s)
- Michał Sobala
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Bożena Bruhn-Olszewska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Michael Cashel
- Intramural Program, Eunice Kennedy Shriver Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Katarzyna Potrykus
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| |
Collapse
|
7
|
Haas TM, Ebensperger P, Eisenbeis VB, Nopper C, Dürr T, Jork N, Steck N, Jessen-Trefzer C, Jessen HJ. Magic spot nucleotides: tunable target-specific chemoenzymatic synthesis. Chem Commun (Camb) 2019; 55:5339-5342. [PMID: 30973558 DOI: 10.1039/c9cc01688k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A tunable chemoenzymatic strategy provides access to the entire class of magic spot nucleotides and modified analogues. The approach combines chemoselective bisphosphorylations using phosphoramidites with regioselective ribonuclease T2 cyclo-phosphate hydrolysis, leading to flexible and simple gram-scale operations.
Collapse
Affiliation(s)
- Thomas M Haas
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany. and Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Paul Ebensperger
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany. and Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Verena B Eisenbeis
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany. and Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Christoph Nopper
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany. and Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Tobias Dürr
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany. and Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Jork
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany. and Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Nicole Steck
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany. and Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | | | - Henning J Jessen
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany. and Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
8
|
Bruhn-Olszewska B, Molodtsov V, Sobala M, Dylewski M, Murakami KS, Cashel M, Potrykus K. Structure-function comparisons of (p)ppApp vs (p)ppGpp for Escherichia coli RNA polymerase binding sites and for rrnB P1 promoter regulatory responses in vitro. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:731-742. [PMID: 30012465 PMCID: PMC6114088 DOI: 10.1016/j.bbagrm.2018.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/03/2018] [Accepted: 07/11/2018] [Indexed: 12/27/2022]
Abstract
Precise regulation of gene expression is crucial for bacteria to respond to changing environmental conditions. In addition to protein factors affecting RNA polymerase (RNAP) activity, second messengers play an important role in transcription regulation, such as well-known effectors of the stringent response: guanosine 5'triphosphate-3'diphosphate and guanosine 3', 5'-bis(diphosphate) [(p)ppGpp]. Although much is known about importance of the 5' and 3' moieties of (p)ppGpp, the role of the guanine base remains somewhat cryptic. Here, we use (p)ppGpp's adenine analogs [(p)ppApp] to investigate how the nucleobase contributes to determine its binding site and transcriptional regulation. We determined X-ray crystal structure of Escherichia coli RNAP-(p)ppApp complex, which shows the analogs bind near the active site and switch regions of RNAP. We have also explored the regulatory effects of (p)ppApp on transcription initiating from the well-studied E. coli rrnB P1 promoter to assess and compare properties of (p)ppApp with (p)ppGpp. We demonstrate that contrary to (p)ppGpp, (p)ppApp activates transcription at this promoter and DksA hinders this effect. Moreover, pppApp exerts a stronger effect than ppApp. We also show that when ppGpp and pppApp are present together, the outcome depends on which one of them was pre-incubated with RNAP first. This behavior suggests a surprising Yin-Yang like reciprocal plasticity of RNAP responses at a single promoter, occasioned simply by pre-exposure to one or the other nucleotide. Our observations underscore the importance of the (p)ppNpp's purine nucleobase for interactions with RNAP, which may lead to a better fundamental understanding of (p)ppGpp regulation of RNAP activity.
Collapse
Affiliation(s)
- Bożena Bruhn-Olszewska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.
| | - Vadim Molodtsov
- Department of Biochemistry and Molecular Biology, Center of RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Michał Sobala
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.
| | - Maciej Dylewski
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, Center of RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Michael Cashel
- Intramural Research Program, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Katarzyna Potrykus
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.
| |
Collapse
|
9
|
Molecular mutagenesis of ppGpp: turning a RelA activator into an inhibitor. Sci Rep 2017; 7:41839. [PMID: 28157202 PMCID: PMC5291098 DOI: 10.1038/srep41839] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/29/2016] [Indexed: 01/26/2023] Open
Abstract
The alarmone nucleotide (p)ppGpp is a key regulator of bacterial metabolism, growth, stress tolerance and virulence, making (p)ppGpp-mediated signaling a promising target for development of antibacterials. Although ppGpp itself is an activator of the ribosome-associated ppGpp synthetase RelA, several ppGpp mimics have been developed as RelA inhibitors. However promising, the currently available ppGpp mimics are relatively inefficient, with IC50 in the sub-mM range. In an attempt to identify a potent and specific inhibitor of RelA capable of abrogating (p)ppGpp production in live bacterial cells, we have tested a targeted nucleotide library using a biochemical test system comprised of purified Escherichia coli components. While none of the compounds fulfilled this aim, the screen has yielded several potentially useful molecular tools for biochemical and structural work.
Collapse
|
10
|
Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance. Microbiol Mol Biol Rev 2016; 81:81/1/e00040-16. [PMID: 28031352 DOI: 10.1128/mmbr.00040-16] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Phosphoribosyl diphosphate (PRPP) is an important intermediate in cellular metabolism. PRPP is synthesized by PRPP synthase, as follows: ribose 5-phosphate + ATP → PRPP + AMP. PRPP is ubiquitously found in living organisms and is used in substitution reactions with the formation of glycosidic bonds. PRPP is utilized in the biosynthesis of purine and pyrimidine nucleotides, the amino acids histidine and tryptophan, the cofactors NAD and tetrahydromethanopterin, arabinosyl monophosphodecaprenol, and certain aminoglycoside antibiotics. The participation of PRPP in each of these metabolic pathways is reviewed. Central to the metabolism of PRPP is PRPP synthase, which has been studied from all kingdoms of life by classical mechanistic procedures. The results of these analyses are unified with recent progress in molecular enzymology and the elucidation of the three-dimensional structures of PRPP synthases from eubacteria, archaea, and humans. The structures and mechanisms of catalysis of the five diphosphoryltransferases are compared, as are those of selected enzymes of diphosphoryl transfer, phosphoryl transfer, and nucleotidyl transfer reactions. PRPP is used as a substrate by a large number phosphoribosyltransferases. The protein structures and reaction mechanisms of these phosphoribosyltransferases vary and demonstrate the versatility of PRPP as an intermediate in cellular physiology. PRPP synthases appear to have originated from a phosphoribosyltransferase during evolution, as demonstrated by phylogenetic analysis. PRPP, furthermore, is an effector molecule of purine and pyrimidine nucleotide biosynthesis, either by binding to PurR or PyrR regulatory proteins or as an allosteric activator of carbamoylphosphate synthetase. Genetic analyses have disclosed a number of mutants altered in the PRPP synthase-specifying genes in humans as well as bacterial species.
Collapse
|
11
|
Choi MY, Wang Y, Wong LLY, Lu BT, Chen WY, Huang JD, Tanner JA, Watt RM. The two PPX-GppA homologues from Mycobacterium tuberculosis have distinct biochemical activities. PLoS One 2012; 7:e42561. [PMID: 22880033 PMCID: PMC3411833 DOI: 10.1371/journal.pone.0042561] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 07/09/2012] [Indexed: 01/26/2023] Open
Abstract
Inorganic polyphosphate (poly-P), guanosine pentaphosphate (pppGpp) and guanosine tetraphosphate (ppGpp) are ubiquitous in bacteria. These molecules play a variety of important physiological roles associated with stress resistance, persistence, and virulence. In the bacterial pathogen Mycobacterium tuberculosis, the identities of the proteins responsible for the metabolism of polyphosphate and (p)ppGpp remain to be fully established. M. tuberculosis encodes two PPX-GppA homologues, Rv0496 (MTB-PPX1) and Rv1026, which share significant sequence similarity with bacterial exopolyphosphatase (PPX) and guanosine pentaphosphate 5′-phosphohydrolase (GPP) proteins. Here we delineate the respective biochemical activities of the Rv0496 and Rv1026 proteins and benchmark these against the activities of the PPX and GPP proteins from Escherichia coli. We demonstrate that Rv0496 functions as an exopolyphosphatase, showing a distinct preference for relatively short-chain poly-P substrates. In contrast, Rv1026 has no detectable exopolyphosphatase activities. Analogous to the E. coli PPX and GPP enzymes, the exopolyphosphatase activities of Rv0496 are inhibited by pppGpp and, to a lesser extent, by ppGpp alarmones, which are produced during the bacterial stringent response. However, neither Rv0496 nor Rv1026 have the ability to hydrolyze pppGpp to ppGpp; a reaction catalyzed by E. coli PPX and GPP. Both the Rv0496 and Rv1026 proteins have modest ATPase and to a lesser extent ADPase activities. pppGpp alarmones inhibit the ATPase activities of Rv1026 and, to a lesser extent, the ATPase activities of Rv0496. We conclude that PPX-GppA family proteins may not possess all the catalytic activities implied by their name and may play distinct biochemical roles involved in polyphosphate and (p)ppGpp metabolic pathways.
Collapse
Affiliation(s)
- Mei Y. Choi
- Oral Biosciences, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Sai Ying Pun, Hong Kong SAR, China
| | - Ying Wang
- Wuhan Centers for Disease Prevention and Control, Wuhan, Hubei Province, China
| | - Leo L. Y. Wong
- Department of Anatomy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Bing-tai Lu
- Oral Biosciences, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Sai Ying Pun, Hong Kong SAR, China
| | - Wen-yang Chen
- Oral Biosciences, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Sai Ying Pun, Hong Kong SAR, China
| | - Jian-Dong Huang
- Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Julian A. Tanner
- Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Rory M. Watt
- Oral Biosciences, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Sai Ying Pun, Hong Kong SAR, China
- * E-mail:
| |
Collapse
|
12
|
Atkinson GC, Tenson T, Hauryliuk V. The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life. PLoS One 2011; 6:e23479. [PMID: 21858139 PMCID: PMC3153485 DOI: 10.1371/journal.pone.0023479] [Citation(s) in RCA: 327] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 07/18/2011] [Indexed: 12/01/2022] Open
Abstract
RelA/SpoT Homologue (RSH) proteins, named for their sequence similarity to the RelA and SpoT enzymes of Escherichia coli, comprise a superfamily of enzymes that synthesize and/or hydrolyze the alarmone ppGpp, activator of the “stringent” response and regulator of cellular metabolism. The classical “long” RSHs Rel, RelA and SpoT with the ppGpp hydrolase, synthetase, TGS and ACT domain architecture have been found across diverse bacteria and plant chloroplasts, while dedicated single domain ppGpp-synthesizing and -hydrolyzing RSHs have also been discovered in disparate bacteria and animals respectively. However, there is considerable confusion in terms of nomenclature and no comprehensive phylogenetic and sequence analyses have previously been carried out to classify RSHs on a genomic scale. We have performed high-throughput sensitive sequence searching of over 1000 genomes from across the tree of life, in combination with phylogenetic analyses to consolidate previous ad hoc identification of diverse RSHs in different organisms and provide a much-needed unifying terminology for the field. We classify RSHs into 30 subgroups comprising three groups: long RSHs, small alarmone synthetases (SASs), and small alarmone hydrolases (SAHs). Members of nineteen previously unidentified RSH subgroups can now be studied experimentally, including previously unknown RSHs in archaea, expanding the “stringent response” to this domain of life. We have analyzed possible combinations of RSH proteins and their domains in bacterial genomes and compared RSH content with available RSH knock-out data for various organisms to determine the rules of combining RSHs. Through comparative sequence analysis of long and small RSHs, we find exposed sites limited in conservation to the long RSHs that we propose are involved in transmitting regulatory signals. Such signals may be transmitted via NTD to CTD intra-molecular interactions, or inter-molecular interactions either among individual RSH molecules or among long RSHs and other binding partners such as the ribosome.
Collapse
|
13
|
Hardiman T, Windeisen V, Ewald JC, Zibek S, Schlack P, Rebell J, Reuss M, Siemann-Herzberg M. In vitro synthesis and characterization of guanosine 3',5'-bis(diphosphate). Anal Biochem 2008; 383:337-9. [PMID: 18789883 DOI: 10.1016/j.ab.2008.07.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Revised: 07/29/2008] [Accepted: 07/30/2008] [Indexed: 10/21/2022]
Abstract
The intracellular alarmone guanosine 3',5'-bis(diphosphate) (ppGpp) has been thoroughly investigated over the past 40 years and has become one of the best-known effectors in bacterial physiology. ppGpp is also of great importance for biotechnological applications. Systems biology research, involving experimental and mathematical approaches, has contributed a great deal to uncovering the alarmone's complex regulatory effects. HPLC analysis and UV detection are used to quantify intracellular ppGpp. The samples analyzed also contain other phosphorylated guanine nucleotides and, therefore, are spiked with a standard ppGpp solution. A rapidly growing number of laboratories are turning to synthesizing the nucleotide in vitro involving time-consuming protocols and yielding only low amounts of ppGpp. The current article provides a protocol for the preparation of large quantities of a ribosome extract that contains high ppGpp synthesis activity. The demonstrated upscaling from shaking flask to bioreactor cultivation involves the continuous and refrigerated harvest of the biomass. (13)C NMR analysis enabled the structural characterization of the synthesis product and was complemented by mass spectrometry and methods that are commonly used to identify ppGpp.
Collapse
Affiliation(s)
- Timo Hardiman
- Institute of Biochemical Engineering, University of Stuttgart, D-70569 Stuttgart, Germany
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Kristensen O, Ross B, Gajhede M. Structure of the PPX/GPPA phosphatase from Aquifex aeolicus in complex with the alarmone ppGpp. J Mol Biol 2007; 375:1469-76. [PMID: 18155044 DOI: 10.1016/j.jmb.2007.11.073] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Revised: 11/21/2007] [Accepted: 11/27/2007] [Indexed: 11/18/2022]
Abstract
The crystal structure of the prototype exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family member from Aquifex aeolicus in complex with the intracellular second messenger guanosine tetraphosphate was determined at 2.7-A resolution. The hydrolytic base is identified as E119. The dual specificity established for the Escherichia coli homolog is shown to be compatible with a common active site for guanosine pentaphosphate and polyphosphate hydrolysis. Distinct and different degrees of closure between the two domains of the enzyme are associated with substrate binding. The arginines R22 and R267, residing in different domains, are crucial for guanosine pentaphosphate specificity as they interact with the unique 3'-ribose phosphorylation.
Collapse
Affiliation(s)
- Ole Kristensen
- Biostructural Research, Department of Medicinal Chemistry, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.
| | | | | |
Collapse
|
15
|
Gabel SA, London RE. Ternary borate-nucleoside complex stabilization by ribonuclease A demonstrates phosphate mimicry. J Biol Inorg Chem 2007; 13:207-17. [PMID: 17957392 DOI: 10.1007/s00775-007-0311-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2007] [Accepted: 10/08/2007] [Indexed: 11/26/2022]
Abstract
Phosphate esters play a central role in cellular energetics, biochemical activation, signal transduction and conformational switching. The structural homology of the borate anion with phosphate, combined with its ability to spontaneously esterify hydroxyl groups, suggested that phosphate ester recognition sites on proteins might exhibit significant affinity for nonenzymatically formed borate esters. (11)B NMR studies and activity measurements on ribonuclease A (RNase A) in the presence of borate and several cytidine analogs demonstrate the formation of a stable ternary RNase A.3'-deoxycytidine-2'-borate ternary complex that mimics the complex formed between RNase A and a 2'-cytidine monophosphate (2'-CMP) inhibitor. Alternatively, no slowly exchanging borate resonance is observed for a ternary RNase A, borate, 2'-deoxycytidine mixture, demonstrating the critical importance of the 2'-hydroxyl group for complex formation. Titration of the ternary complex with 2'-CMP shows that it can displace the bound borate ester with a binding constant that is close to the reported inhibition constant of RNase A by 2'-CMP. RNase A binding of a cyclic cytidine-2',3'-borate ester, which is a structural homolog of the cytidine-2',3'-cyclic phosphate substrate, could also be demonstrated. The apparent dissociation constant for the cytidine-2',3'-borate.RNase A complex is 0.8 mM, which compares with a Michaelis constant of 11 mM for cytidine-2',3'-cyclic phosphate at pH 7, indicating considerably stronger binding. However, the value is 1,000-fold larger than the reported dissociation constant of the RNase A complex with uridine-vanadate. These results are consistent with recent reports suggesting that in situ formation of borate esters that mimic the corresponding phosphate esters supports enzyme catalysis.
Collapse
Affiliation(s)
- Scott A Gabel
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | | |
Collapse
|
16
|
Kasai K, Nishizawa T, Takahashi K, Hosaka T, Aoki H, Ochi K. Physiological analysis of the stringent response elicited in an extreme thermophilic bacterium, Thermus thermophilus. J Bacteriol 2006; 188:7111-22. [PMID: 17015650 PMCID: PMC1636220 DOI: 10.1128/jb.00574-06] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Guanosine tetraphosphate (ppGpp) is a key mediator of stringent control, an adaptive response of bacteria to amino acid starvation, and has thus been termed a bacterial alarmone. Previous X-ray crystallographic analysis has provided a structural basis for the transcriptional regulation of RNA polymerase activity by ppGpp in the thermophilic bacterium Thermus thermophilus. Here we investigated the physiological basis of the stringent response by comparing the changes in intracellular ppGpp levels and the rate of RNA synthesis in stringent (rel(+); wild type) and relaxed (relA and relC; mutant) strains of T. thermophilus. We found that in wild-type T. thermophilus, as in other bacteria, serine hydroxamate, an amino acid analogue that inhibits tRNA(Ser) aminoacylation, elicited a stringent response characterized in part by intracellular accumulation of ppGpp and that this response was completely blocked in a relA-null mutant and partially blocked in a relC mutant harboring a mutation in the ribosomal protein L11. Subsequent in vitro assays using ribosomes isolated from wild-type and relA and relC mutant strains confirmed that (p)ppGpp is synthesized by ribosomes and that mutation of RelA or L11 blocks that activity. This conclusion was further confirmed in vitro by demonstrating that thiostrepton or tetracycline inhibits (p)ppGpp synthesis. In an in vitro system, (p)ppGpp acted by inhibiting RNA polymerase-catalyzed 23S/5S rRNA gene transcription but at a concentration much higher than that of the observed intracellular ppGpp pool size. On the other hand, changes in the rRNA gene promoter activity tightly correlated with changes in the GTP but not ATP concentration. Also, (p)ppGpp exerted a potent inhibitory effect on IMP dehydrogenase activity. The present data thus complement the earlier structural analysis by providing physiological evidence that T. thermophilus does produce ppGpp in response to amino acid starvation in a ribosome-dependent (i.e., RelA-dependent) manner. However, it appears that in T. thermophilus, rRNA promoter activity is controlled directly by the GTP pool size, which is modulated by ppGpp via inhibition of IMP dehydrogenase activity. Thus, unlike the case of Escherichia coli, ppGpp may not inhibit T. thermophilus RNA polymerase activity directly in vivo, as recently proposed for Bacillus subtilis rRNA transcription (L. Krasny and R. L. Gourse, EMBO J. 23:4473-4483, 2004).
Collapse
MESH Headings
- Adaptation, Physiological
- Adenosine Triphosphate/metabolism
- Amino Acid Sequence
- Anti-Bacterial Agents/pharmacology
- Bacterial Proteins/genetics
- DNA-Directed RNA Polymerases/antagonists & inhibitors
- DNA-Directed RNA Polymerases/metabolism
- Gene Expression Regulation, Bacterial
- Guanosine Tetraphosphate/metabolism
- Guanosine Triphosphate/physiology
- IMP Dehydrogenase/antagonists & inhibitors
- IMP Dehydrogenase/metabolism
- Ligases/genetics
- Ligases/metabolism
- Molecular Sequence Data
- Mutation
- Promoter Regions, Genetic
- RNA, Bacterial/biosynthesis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 23S/biosynthesis
- RNA, Ribosomal, 5S/biosynthesis
- Ribosomal Proteins/genetics
- Ribosomes/physiology
- Sequence Alignment
- Serine/analogs & derivatives
- Serine/pharmacology
- Tetracycline/pharmacology
- Thermus thermophilus/genetics
- Thermus thermophilus/growth & development
- Thermus thermophilus/metabolism
- Thermus thermophilus/physiology
- Thiostrepton/pharmacology
- Transcription, Genetic
- Uracil/metabolism
Collapse
Affiliation(s)
- Koji Kasai
- National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | | | | | | | | | | |
Collapse
|
17
|
|
18
|
Artsimovitch I, Patlan V, Sekine SI, Vassylyeva MN, Hosaka T, Ochi K, Yokoyama S, Vassylyev DG. Structural basis for transcription regulation by alarmone ppGpp. Cell 2004; 117:299-310. [PMID: 15109491 DOI: 10.1016/s0092-8674(04)00401-5] [Citation(s) in RCA: 217] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2003] [Revised: 02/23/2004] [Accepted: 02/24/2004] [Indexed: 11/19/2022]
Abstract
Guanosine-tetraphosphate (ppGpp) is a major regulator of stringent control, an adaptive response of bacteria to amino acid starvation. The 2.7 A resolution structure of the Thermus thermophilus RNA polymerase (RNAP) holoenzyme in complex with ppGpp reveals that ppGpp binds to the same site near the active center in both independent RNAP molecules in the crystal but in strikingly distinct orientations. Binding is symmetrical with respect to the two diphosphates of ppGpp and is relaxed with respect to the orientation of the nucleotide base. Different modes of ppGpp binding are coupled with asymmetry of the active site configurations. The results suggest that base pairing of ppGpp with cytosines in the nontemplate DNA strand might be an essential component of transcription control by ppGpp. We present experimental evidence highlighting the importance of base-specific contacts between ppGpp and specific cytosine residues during both transcription initiation and elongation.
Collapse
Affiliation(s)
- Irina Artsimovitch
- Department of Microbiology, Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Greenwood RC, Gentry DR. The effect of antibiotic treatment on the intracellular nucleotide pools of Staphylococcus aureus. FEMS Microbiol Lett 2002; 208:203-6. [PMID: 11959437 DOI: 10.1111/j.1574-6968.2002.tb11082.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In an assessment of antibiotic action on Staphylococcus aureus, we found that distinct changes in intracellular nucleotide pools occur depending on the antibiotic mode of action. In particular, we have quantitated the effect of antibiotics on pools of the nucleotide guanosine 3'-diphosphate, 5'-triphosphate (pppGpp). Intracellular pppGpp levels increased in response to treatment with the isoleucyl tRNA synthetase inhibitor mupirocin, the uncoupler carbonyl cyanide-m-chlorophenylhydrazone, and rifampicin. These compounds were distinguishable by the degree in which they increased the pppGpp pool and by their differential effect on the pools of other nucleotides. This technique has been used to confirm and to refute the expected mode of action of several compounds identified as possible inhibitors of tRNA synthetases. Our results provide the framework for using nucleotide analysis in the assessment of novel antimicrobial compounds with unknown modes of action.
Collapse
Affiliation(s)
- Rebecca C Greenwood
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA 19426-0989, USA
| | | |
Collapse
|
20
|
Ochi K. Thetsrgene-coding plasmid pIJ702 prevents thiopeptin from inhibiting ppGpp synthesis inStreptomyces lividans. FEMS Microbiol Lett 1989. [DOI: 10.1111/j.1574-6968.1989.tb03582.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
21
|
Mukai J, Muta S, Ozumi Y. Streptomyces nucleotide 3'-pyrophosphokinase are insensitive to stringent control. J Basic Microbiol 1989; 29:671-4. [PMID: 2561157 DOI: 10.1002/jobm.3620291008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The synthesis of GTP- and ATP-3'-pyrophosphate by Streptomyces morookaensis nucleotide 3'-pyrophosphokinase was little affected by the presence of a ribosome-deacylated tRNA-poly A, G, U mixture in vitro. The Streptomyces pyrophosphokinases thus do not appear, unlike bacterial stringent factors, to play a significant role in the cellular stringent control.
Collapse
Affiliation(s)
- J Mukai
- Graduate School of Genetic Resources Technology, Kyushu University, Fukuoka, Japan
| | | | | |
Collapse
|
22
|
Riedel K. [Nucleoside polyphosphates: occurrence, metabolism and function]. ZEITSCHRIFT FUR ALLGEMEINE MIKROBIOLOGIE 1983; 23:103-41. [PMID: 6346704 DOI: 10.1002/jobm.3630230206] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Procaryotes have regulatory systems allowing to vary the metabolism in response to nutritional variations, to reduce the growth, and to start development. Nucleoside polyphosphates are mediators of coordinated alterations of metabolism. In this review, after a brief recall of the characteristics of the stringent response, the occurrence, determinations, and the metabolism of the nucleoside polyphosphates are presented. The representation of the pleiotropic effects includes the regulation of the protein synthesis and of the protein synthesis apparatus, of the protein turnover, of the N- and carbohydrate metabolism, of the formation of cell membranes and cell walls as well as the possible function of the development.
Collapse
|
23
|
Hamagishi Y, Yoshimoto A, Oki T. Determination of guanosine tetraphosphate (ppGpp) and adenosine pentaphosphate (pppApp) in various microorganisms by radioimmunoassay. Arch Microbiol 1981. [DOI: 10.1007/bf00411065] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
24
|
Hamagishi Y, Tone H, Oki T, Inui T. Effect of adenosine-5'-triphosphate-3'-diphosphate and related nucleoside polyphosphates on the spore germination of Streptomyces galilaeus. Arch Microbiol 1980; 125:285-9. [PMID: 6155110 DOI: 10.1007/bf00446889] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Exogenous addition of adenosine- and guanosine 5'-(di- and tri) phosphate 3'-diphosphate (pppApp, ppApp, pppGpp and ppGpp) at the concentration of 0.5 mM inhibits spore germination of Streptomyces galilaeus ATCC 31133. This reversible inhibitory effect appeared to be at the transcriptional level, and also depends on the phase of spore germination; pppApp inhibited more strongly RNA synthesis in the period of the germ tube emergence than the early stage of germination. No inhibitory effect was observed with normal purine and pyrimidine nucleosides, nucleotides, pApp, pGpp, cyclic AMP and pyrophosphoric acid at the concentration of 0.1 - 1.0 mM.
Collapse
|
25
|
Richter D, Fehr S, Harder R. The guanosine 3',5'-bis(diphosphate) (ppGpp) cycle. Comparison of synthesis and degradation of guanosine 3',5'-bis(diphosphate) in various bacterial systems. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 99:57-64. [PMID: 114395 DOI: 10.1111/j.1432-1033.1979.tb13230.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
26
|
Genetics of Industrial Microorganisms. ACTA ACUST UNITED AC 1979. [DOI: 10.1016/b978-0-12-040303-5.50008-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|
27
|
Fehr S, Godt F, Isono K, Richter D. A ribosome-independent stringent factor from Bacillus stearothermophilus and a low molecular weight substance inhibitory to its activity. FEBS Lett 1979; 97:91-5. [PMID: 216581 DOI: 10.1016/0014-5793(79)80059-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
28
|
Yoshimoto A, Oki T, Inui T. Effect of guanosine 5'-diphosphate 3'-diphosphate and related nucleoside polyphosphates on induction of tryptophanase and beta-galactosidase in permeabilized cells of Escherichia coli. Arch Microbiol 1978; 119:81-6. [PMID: 214051 DOI: 10.1007/bf00407932] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Exogenous addition of guanosine and adenosine 5'-(mono, di and tri) phosphate 3'-diphosphates (pppGpp, ppGpp, pGpp, pppApp, ppApp and pApp) stimulated the synthesis of tryptophanase and beta-galactosidase in permeabilized cells of Escherichia coli. From the results obtained with ppGpp and pppApp, this effect appeared to be at a transcriptional level and depended greatly on the growth condition; the largest effect was observed in cells under shiftdown or grown on poor enrgy source. ppGpp and pppApp, unlike cyclic AMP, did not act to overcome the inhibition of enzyme induction by glucose, but in combination with cyclic AMP caused a synergistic stimulation effect. In the shiftdown cells, ppGpp and pppApp gave 30% or more stimulation effect on tryptophanase induction while cyclic AMP did not stimulate induction. There was therefore a pronounced difference between cyclic AMP and ppGpp or pppApp in stimulatory function.
Collapse
|
29
|
Rhaese HJ, Groscurth R. Studies on the control of development. Synthesis of two highly phosphorylated nucleotides depends on changes in the composition of ribosomes at the beginning of sporulation in Bacillus subtilis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 85:517-28. [PMID: 417920 DOI: 10.1111/j.1432-1033.1978.tb12267.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
30
|
Zabos P, Bauer P, Schlotthauer J, Horváth I. Stringent factor-independent synthesis of pppGpp in Escherichia coli strains. FEBS Lett 1976; 64:107-10. [PMID: 773696 DOI: 10.1016/0014-5793(76)80261-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
31
|
Oki T, Yoshimoto A, Ogasawara T, Sato S, Takamatsu A. Occurrence of pppApp-synthesizing activity in actinomycetes and isolation of purine nucleotide pyrophosphotransferase. Arch Microbiol 1976; 107:183-7. [PMID: 1259517 DOI: 10.1007/bf00446837] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The occurrence of adenosine 5'-triphosphate-3'diphosphate-synthesizing activity was detected in five strains of actinomycetes; Streptomyces morookaensis, Streptomyces aspergilloides, Streptomyces hachijoensis, tactinomyces violascens and Streptoverticillium septatum, out of 825 strains of actinomycetes, bacteria, fungi and fungi imperficti. Purine nucleotide pyrophosphotransferase were extracellularly excreted associating with the cell growth, and were purified partially or to apparent homogeneiety from the culture filtrate. The enzymes are a monomeric protein with molecular weight of 18,000-26,000 and synthesize adenosine, guanosine and inosine 5'-phosphate (mono, di or tri)-3'-diphosphate such as pApp, ppA pp, pppApp, pGpp, ppGpp, pppGpp, and pppIpp by transferring a pyrophosphoryl group from the 5'-position of ATP, dATP and ppApp to the 3'-position of purine nucleotides in the presence of a divalent cation and in alkaline state.
Collapse
|