1
|
Yao Y, Sun H, Wurihan, Gegeheng, Gezi, Skarstad K, Fan L, Morigen. A DnaA-dependent riboswitch for transcription attenuation of the his operon. MLIFE 2023; 2:126-140. [PMID: 38817620 PMCID: PMC10989985 DOI: 10.1002/mlf2.12075] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 06/04/2023] [Indexed: 06/01/2024]
Abstract
Transcription attenuation in response to the availability of a specific amino acid is believed to be controlled by alternative configurations of RNA secondary structures that lead to the arrest of translation or the release of the arrested ribosome from the leader mRNA molecule. In this study, we first report a possible example of the DnaA-dependent riboswitch for transcription attenuation in Escherichia coli. We show that (i) DnaA regulates the transcription of the structural genes but not that of the leader hisL gene; (ii) DnaA might bind to rDnaA boxes present in the HisL-SL RNA, and subsequently attenuate the transcription of the operon; (iii) the HisL-SL RNA and rDnaA boxes are phylogenetically conserved and evolutionarily important; and (iv) the translating ribosome is required for deattenuation of the his operon, whereas tRNAHis strengthens attenuation. This mechanism seems to be phylogenetically conserved in Gram-negative bacteria and evolutionarily important.
Collapse
Affiliation(s)
- Yuan Yao
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Hongwei Sun
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Wurihan
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Gegeheng
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Gezi
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Kirsten Skarstad
- Department of Molecular Cell Biology and Department of MicrobiologyOslo University HospitalOsloNorway
| | - Lifei Fan
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Morigen
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| |
Collapse
|
2
|
Fernández-Coll L, Cashel M. Contributions of SpoT Hydrolase, SpoT Synthetase, and RelA Synthetase to Carbon Source Diauxic Growth Transitions in Escherichia coli. Front Microbiol 2018; 9:1802. [PMID: 30123210 PMCID: PMC6085430 DOI: 10.3389/fmicb.2018.01802] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/17/2018] [Indexed: 12/22/2022] Open
Abstract
During the diauxic shift, Escherichia coli exhausts glucose and adjusts its expression pattern to grow on a secondary carbon source. Transcriptional profiling studies of glucose–lactose diauxic transitions reveal a key role for ppGpp. The amount of ppGpp depends on RelA synthetase and the balance between a strong SpoT hydrolase and its weak synthetase. In this study, mutants are used to search for synthetase or hydrolase specific regulation. Diauxic shifts experiments were performed with strains containing SpoT hydrolase and either RelA or SpoT synthetase as the sole source of ppGpp. Here, the length of the diauxic lag times is determined by the presence of ppGpp, showing contributions of both ppGpp synthetases (RelA and SpoT) as well as its hydrolase (SpoT). A balanced ppGpp response is key for a proper adaptation during diauxic shift. The effects of one or the other ppGpp synthetase on diauxic shifts are abolished by addition of amino acids or succinate, although by different mechanisms. While amino acids control the RelA response, succinate blocks the uptake of the excreted acetate via SatP. Acetate is converted to Acetyl-CoA through the ackA-pta pathway, producing Ac-P as intermediate. Evidence of control of the ackA-pta operon as well as a correlation between ppGpp and Ac-P is shown. Finally, acetylation of proteins is shown to occur during a diauxic glucose–lactose shift.
Collapse
Affiliation(s)
- Llorenç Fernández-Coll
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Michael Cashel
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
3
|
Abstract
The biosynthesis of histidine in Escherichia coli and Salmonella typhimurium has been an important model system for the study of relationships between the flow of intermediates through a biosynthetic pathway and the control of the genes encoding the enzymes that catalyze the steps in a pathway. This article provides a comprehensive review of the histidine biosynthetic pathway and enzymes, including regulation of the flow of intermediates through the pathway and mechanisms that regulate the amounts of the histidine biosynthetic enzymes. In addition, this article reviews the structure and regulation of the histidine (his) biosynthetic operon, including transcript processing, Rho-factor-dependent "classical" polarity, and the current model of his operon attenuation control. Emphasis is placed on areas of recent progress. Notably, most of the enzymes that catalyze histidine biosynthesis have recently been crystallized, and their structures have been determined. Many of the histidine biosynthetic intermediates are unstable, and the histidine biosynthetic enzymes catalyze some chemically unusual reactions. Therefore, these studies have led to considerable mechanistic insight into the pathway itself and have provided deep biochemical understanding of several fundamental processes, such as feedback control, allosteric interactions, and metabolite channeling. Considerable recent progress has also been made on aspects of his operon regulation, including the mechanism of pp(p)Gpp stimulation of his operon transcription, the molecular basis for transcriptional pausing by RNA polymerase, and pathway evolution. The progress in these areas will continue as sophisticated new genomic, metabolomic, proteomic, and structural approaches converge in studies of the histidine biosynthetic pathway and mechanisms of control of his biosynthetic genes in other bacterial species.
Collapse
|
4
|
Erdogan I, Akcelik N, Akcelik M. Comparative proteomic analysis of Salmonella typhimurium LT2 and its hisG gene inactivated mutant. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2015. [DOI: 10.3103/s0891416815010024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
5
|
Ramachandran VK, Shearer N, Jacob JJ, Sharma CM, Thompson A. The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression. BMC Genomics 2012; 13:25. [PMID: 22251276 PMCID: PMC3293720 DOI: 10.1186/1471-2164-13-25] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 01/17/2012] [Indexed: 11/26/2022] Open
Abstract
Background Invasion of intestinal epithelial cells by Salmonella enterica serovar Typhimurium (S. Typhimurium) requires expression of the extracellular virulence gene expression programme (STEX), activation of which is dependent on the signalling molecule guanosine tetraphosphate (ppGpp). Recently, next-generation transcriptomics (RNA-seq) has revealed the unexpected complexity of bacterial transcriptomes and in this report we use differential RNA sequencing (dRNA-seq) to define the high-resolution transcriptomic architecture of wild-type S. Typhimurium and a ppGpp null strain under growth conditions which model STEX. In doing so we show that ppGpp plays a much wider role in regulating the S. Typhimurium STEX primary transcriptome than previously recognised. Results Here we report the precise mapping of transcriptional start sites (TSSs) for 78% of the S. Typhimurium open reading frames (ORFs). The TSS mapping enabled a genome-wide promoter analysis resulting in the prediction of 169 alternative sigma factor binding sites, and the prediction of the structure of 625 operons. We also report the discovery of 55 new candidate small RNAs (sRNAs) and 302 candidate antisense RNAs (asRNAs). We discovered 32 ppGpp-dependent alternative TSSs and determined the extent and level of ppGpp-dependent coding and non-coding transcription. We found that 34% and 20% of coding and non-coding RNA transcription respectively was ppGpp-dependent under these growth conditions, adding a further dimension to the role of this remarkable small regulatory molecule in enabling rapid adaptation to the infective environment. Conclusions The transcriptional architecture of S. Typhimurium and finer definition of the key role ppGpp plays in regulating Salmonella coding and non-coding transcription should promote the understanding of gene regulation in this important food borne pathogen and act as a resource for future research.
Collapse
Affiliation(s)
- Vinoy K Ramachandran
- Institute of Food Research, Norwich, UK, University of Würzburg, Josef-Schneider-Str, 2/Bau D15, 97080 Würzburg, Germany
| | | | | | | | | |
Collapse
|
6
|
Edwards AN, Patterson-Fortin LM, Vakulskas CA, Mercante JW, Potrykus K, Vinella D, Camacho MI, Fields JA, Thompson SA, Georgellis D, Cashel M, Babitzke P, Romeo T. Circuitry linking the Csr and stringent response global regulatory systems. Mol Microbiol 2011; 80:1561-80. [PMID: 21488981 DOI: 10.1111/j.1365-2958.2011.07663.x] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CsrA protein regulates important cellular processes by binding to target mRNAs and altering their translation and/or stability. In Escherichia coli, CsrA binds to sRNAs, CsrB and CsrC, which sequester CsrA and antagonize its activity. Here, mRNAs for relA, spoT and dksA of the stringent response system were found among 721 different transcripts that copurified with CsrA. Many of the transcripts that copurified with CsrA were previously determined to respond to ppGpp and/or DksA. We examined multiple regulatory interactions between the Csr and stringent response systems. Most importantly, DksA and ppGpp robustly activated csrB/C transcription (10-fold), while they modestly activated csrA expression. We propose that CsrA-mediated regulation is relieved during the stringent response. Gel shift assays confirmed high affinity binding of CsrA to relA mRNA leader and weaker interactions with dksA and spoT. Reporter fusions, qRT-PCR and immunoblotting showed that CsrA repressed relA expression, and (p)ppGpp accumulation during stringent response was enhanced in a csrA mutant. CsrA had modest to negligible effects on dksA and spoT expression. Transcription of dksA was negatively autoregulated via a feedback loop that tended to mask CsrA effects. We propose that the Csr system fine-tunes the stringent response and discuss biological implications of the composite circuitry.
Collapse
Affiliation(s)
- Adrianne N Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Abstract
The biosynthesis of histidine in Escherichia coli and Salmonella typhimurium has been an important model system for the study of relationships between the flow of intermediates through a biosynthetic pathway and the control of the genes encoding the enzymes that catalyze the steps in a pathway. This article provides a comprehensive review of the histidine biosynthetic pathway and enzymes, including regulation of the flow of intermediates through the pathway and mechanisms that regulate the amounts of the histidine biosynthetic enzymes. In addition, this article reviews the structure and regulation of the histidine (his) biosynthetic operon, including transcript processing, Rho-factor-dependent "classical" polarity, and the current model of his operon attenuation control. Emphasis is placed on areas of recent progress. Notably, most of the enzymes that catalyze histidine biosynthesis have recently been crystallized, and their structures have been determined. Many of the histidine biosynthetic intermediates are unstable, and the histidine biosynthetic enzymes catalyze some chemically unusual reactions. Therefore, these studies have led to considerable mechanistic insight into the pathway itself and have provided deep biochemical understanding of several fundamental processes, such as feedback control, allosteric interactions, and metabolite channeling. Considerable recent progress has also been made on aspects of his operon regulation, including the mechanism of pp(p)Gpp stimulation of his operon transcription, the molecular basis for transcriptional pausing by RNA polymerase, and pathway evolution. The progress in these areas will continue as sophisticated new genomic, metabolomic, proteomic, and structural approaches converge in studies of the histidine biosynthetic pathway and mechanisms of control of his biosynthetic genes in other bacterial species.
Collapse
|
8
|
Bougdour A, Gottesman S. ppGpp regulation of RpoS degradation via anti-adaptor protein IraP. Proc Natl Acad Sci U S A 2007; 104:12896-901. [PMID: 17640895 PMCID: PMC1937563 DOI: 10.1073/pnas.0705561104] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
IraP is a small protein that interferes with the delivery of sigma(S) (RpoS) to the ClpXP protease by blocking the action of RssB, an adaptor protein for sigma(S) degradation. IraP was previously shown to mediate stabilization of sigma(S) during phosphate starvation. Here, we show that iraP is transcribed in response to phosphate starvation; this response is mediated by ppGpp. The iraP promoter is positively regulated by ppGpp, dependent on the discriminator region of the iraP promoter. Sensing of phosphate starvation requires SpoT but not RelA. The results demonstrate a target for positive regulation by ppGpp and suggest that the cell use of ppGpp to mediate a variety of starvation responses operates in part by modulating sigma(S) levels.
Collapse
Affiliation(s)
- Alexandre Bougdour
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
9
|
Thompson A, Rolfe MD, Lucchini S, Schwerk P, Hinton JCD, Tedin K. The bacterial signal molecule, ppGpp, mediates the environmental regulation of both the invasion and intracellular virulence gene programs of Salmonella. J Biol Chem 2006; 281:30112-21. [PMID: 16905537 DOI: 10.1074/jbc.m605616200] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
During infection of mammalian hosts, facultative intracellular pathogens have to adjust rapidly to different environmental conditions encountered during passage through the gastrointestinal tract and following uptake into epithelial cells and macrophages. Successful establishment within the host therefore requires the coordinated expression of a large number of virulence genes necessary for the adaptation between the extracellular and intracellular phases of infection. In this study we show that the bacterial signal molecule, ppGpp, plays a major role in mediating the environmental signals involved in the regulation of both the extracellular and intracellular virulence gene programs. Under oxygen limiting conditions, we observed a strong ppGpp dependence for invasion gene expression, the result of severe reductions in expression of the Salmonella pathogenicity island (SPI) 1 transcriptional regulator genes hilA, C, and D and invF. Overexpression of the non-SPI1-encoded regulator RtsA restored hilA expression in the absence of ppGpp. SPI2-encoded genes, required for intracellular proliferation in macrophages, were activated in the wild type strain under aerobic, late log phase growth conditions. The expression of SPI2 genes was also shown to be ppGpp-dependent under these conditions. The results from this study suggest a mechanism for the alternate regulation of the opposing extracellular and intracellular virulence gene programs and indicate a remarkable specificity for ppGpp in the regulation of genes involved in virulence compared with the rest of the genome. This is the first demonstration that this highly conserved regulatory system is involved in bacterial virulence gene expression on a global scale.
Collapse
Affiliation(s)
- Arthur Thompson
- Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom.
| | | | | | | | | | | |
Collapse
|
10
|
Nyström T. Growth versus maintenance: a trade-off dictated by RNA polymerase availability and sigma factor competition? Mol Microbiol 2005; 54:855-62. [PMID: 15522072 DOI: 10.1111/j.1365-2958.2004.04342.x] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The regulatory design of higher organisms is proposed to comprise a trade-off between activities devoted to reproduction and those devoted to cellular maintenance and repair. Excessive reproduction will inevitably limit the organism's ability to resist stress whereas excessively devoted stress defence systems may increase lifespan but reduce Darwinian fitness. The trade-off is arguably a consequence of limited resources in any one organism but the nature and identity of such limiting resources are ambiguous. Analysis of global control of gene expression in Escherichia coli suggests that reproduction and maintenance activities are also at odds in bacteria and that this antagonism may be a consequence of a battle between transcription factors for limiting RNA polymerase. The outcome of this battle is regulated and depends on the nutritional status of the environment, the levels of the alarmone ppGpp, and RNA polymerase availability. This paper reviews how the concentration of RNA polymerase available for transcription initiation may vary upon shifts between growth and growth-arrest conditions and how this adjustment may differentially affect genes whose functions relate to reproduction and maintenance.
Collapse
Affiliation(s)
- Thomas Nyström
- Department of Cell and Molecular Biology - Microbiology, Göteborg University, Medicinaregatan 9C, 413 90 Göteborg, Sweden.
| |
Collapse
|
11
|
Paul BJ, Berkmen MB, Gourse RL. DksA potentiates direct activation of amino acid promoters by ppGpp. Proc Natl Acad Sci U S A 2005; 102:7823-8. [PMID: 15899978 PMCID: PMC1142371 DOI: 10.1073/pnas.0501170102] [Citation(s) in RCA: 255] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Amino acid starvation in Escherichia coli results in a spectrum of changes in gene expression, including inhibition of rRNA and tRNA promoters and activation of certain promoters for amino acid biosynthesis and transport. The unusual nucleotide ppGpp plays an important role in both negative and positive regulation. Previously, we and others suggested that positive effects of ppGpp might be indirect, resulting from the inhibition of rRNA transcription and, thus, liberation of RNA polymerase for binding to other promoters. Recently, we showed that DksA binds to RNA polymerase and greatly enhances direct effects of ppGpp on the negative control of rRNA promoters. This conclusion prompted us to reevaluate whether ppGpp might also have a direct role in positive control. We show here that ppGpp greatly increases the rate of transcription initiation from amino acid promoters in a purified system but only when DksA is present. Activation occurs by stimulation of the rate of an isomerization step on the pathway to open complex formation. Consistent with the model that ppGpp/DksA stimulates amino acid promoters both directly and indirectly in vivo, cells lacking dksA fail to activate transcription from the hisG promoter after amino acid starvation. Our results illustrate how transcription factors can positively regulate transcription initiation without binding DNA, demonstrate that dksA directly affects promoters in addition to those for rRNA, and suggest that some of the pleiotropic effects previously associated with dksA might be ascribable to direct effects of dksA on promoters involved in a wide variety of cellular functions.
Collapse
Affiliation(s)
- Brian J Paul
- Department of Bacteriology, University of Wisconsin, 420 Henry Mall, Madison, WI 53706, USA
| | | | | |
Collapse
|
12
|
Travers A, Muskhelishvili G. DNA supercoiling — a global transcriptional regulator for enterobacterial growth? Nat Rev Microbiol 2005; 3:157-69. [PMID: 15685225 DOI: 10.1038/nrmicro1088] [Citation(s) in RCA: 244] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A fundamental principle of exponential bacterial growth is that no more ribosomes are produced than are necessary to support the balance between nutrient availability and protein synthesis. Although this conclusion was first expressed more than 40 years ago, a full understanding of the molecular mechanisms involved remains elusive and the issue is still controversial. There is currently agreement that, although many different systems are undoubtedly involved in fine-tuning this balance, an important control, and in our opinion perhaps the main control, is regulation of the rate of transcription initiation of the stable (ribosomal and transfer) RNA transcriptons. In this review, we argue that regulation of DNA supercoiling provides a coherent explanation for the main modes of transcriptional control - stringent control, growth-rate control and growth-phase control - during the normal growth of Escherichia coli.
Collapse
Affiliation(s)
- Andrew Travers
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
| | | |
Collapse
|
13
|
Pizarro-Cerdá J, Tedin K. The bacterial signal molecule, ppGpp, regulates Salmonella virulence gene expression. Mol Microbiol 2005; 52:1827-44. [PMID: 15186428 DOI: 10.1111/j.1365-2958.2004.04122.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Numerous, overlapping global regulatory systems mediate the environmental signalling controlling the virulence of Salmonella typhimurium. With both extra- and intracellular lifestyles, unravelling the mechanisms involved in regulating Salmonella pathogenesis has been complex. Here, we report a factor co-ordinating environmental signals with global regulators involved in pathogenesis. An S. typhimuriumDeltarelADeltaspoT strain deficient in guanosine tetraphosphate (ppGpp) synthesis was found to be highly attenuated in vivo and non-invasive in vitro. The DeltarelADeltaspoT strain exhibited severely reduced expression of hilA and invF, encoding major transcriptional activators required for Salmonella pathogenicity island 1 (SPI-1) gene expression and at least two other pathogenicity islands. None of the growth conditions intended to mimic the intestinal milieu was capable of inducing hilA expression in the absence of ppGpp. However, the expression of global regulators of Salmonella virulence, RpoS and PhoP/Q, and RpoS- and PhoP/Q-dependent, non-virulence-related genes was not significantly different from the wild-type strain. The results indicate that ppGpp plays a central role as a regulator of virulence gene expression in S. typhimurium and implicates ppGpp as a major factor in the environmental and host-dependent regulation of Salmonella pathogenesis.
Collapse
Affiliation(s)
- Javier Pizarro-Cerdá
- Institut Pasteur, Unité Interactions Bactéries-Cellules, 28 Rue du Docteur Roux, F-75724 Cedex 15 Paris, France
| | | |
Collapse
|
14
|
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
|
15
|
Song M, Kim HJ, Kim EY, Shin M, Lee HC, Hong Y, Rhee JH, Yoon H, Ryu S, Lim S, Choy HE. ppGpp-dependent stationary phase induction of genes on Salmonella pathogenicity island 1. J Biol Chem 2004; 279:34183-90. [PMID: 15161921 DOI: 10.1074/jbc.m313491200] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have examined expression of the genes on Salmonella pathogenicity island 1 (SPI1) during growth under the physiologically well defined standard growth condition of Luria-Bertani medium with aeration. We found that the central regulator hilA and the genes under its control are expressed at the onset of stationary phase. Interestingly, the two-component regulatory genes hilC/hilD, sirA/barA, and ompR, which are known to modulate expression from the hilA promoter (hilAp) under so-called "inducing conditions" (Luria-Bertani medium containing 0.3 m NaCl without aeration), acted under standard conditions at the stationary phase induction level. The induction of hilAp depended not on RpoS, the stationary phase sigma factor, but on the stringent signal molecule ppGpp. In the ppGpp null mutant background, hilAp showed absolutely no activity. The stationary phase induction of hilAp required spoT but not relA. Consistent with this requirement, hilAp was also induced by carbon source deprivation, which is known to transiently elevate ppGpp mediated by spoT function. The observation that amino acid starvation elicited by the addition of serine hydroxamate did not induce hilAp in a RelA(+) SpoT(+) strain suggested that, in addition to ppGpp, some other alteration accompanying entry into the stationary phase might be necessary for induction. It is speculated that during the course of infection Salmonella encounters various stressful environments that are sensed and translated to the intracellular signal, ppGpp, which allows expression of Salmonella virulence genes, including SPI1 genes.
Collapse
Affiliation(s)
- Miryoung Song
- Genome Research Center for Enteropathogenic Bacteria and Research Institute of Vibrio Infection, Chonnam National University Medical College, Kwangju 501-746, South Korea
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Jishage M, Kvint K, Shingler V, Nyström T. Regulation of sigma factor competition by the alarmone ppGpp. Genes Dev 2002; 16:1260-70. [PMID: 12023304 PMCID: PMC186289 DOI: 10.1101/gad.227902] [Citation(s) in RCA: 278] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Many regulons controlled by alternative sigma factors, including sigma(S) and sigma(32), are poorly induced in cells lacking the alarmone ppGpp. We show that ppGpp is not absolutely required for the activity of sigma(S)-dependent promoters because underproduction of sigma(70), specific mutations in rpoD (rpoD40 and rpoD35), or overproduction of Rsd (anti-sigma(70)) restored expression from sigma(S)-dependent promoters in vivo in the absence of ppGpp accumulation. An in vitro transcription/competition assay with reconstituted RNA polymerase showed that addition of ppGpp reduces the ability of wild-type sigma(70) to compete with sigma(32) for core binding and the mutant sigma(70) proteins, encoded by rpoD40 and rpoD35, compete less efficiently than wild-type sigma(70). Similarly, an in vivo competition assay showed that the ability of both sigma(32) and sigma(S) to compete with sigma(70) is diminished in cells lacking ppGpp. Consistently, the fraction of sigma(S) and sigma(32) bound to core was drastically reduced in ppGpp-deficient cells. Thus, the stringent response encompasses a mechanism that alters the relative competitiveness of sigma factors in accordance with cellular demands during physiological stress.
Collapse
Affiliation(s)
- Miki Jishage
- Department of Cell and Molecular Biology-Microbiology, Göteborg University, 405 30 Göteberg, Sweden
| | | | | | | |
Collapse
|
17
|
Eymann C, Homuth G, Scharf C, Hecker M. Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis. J Bacteriol 2002; 184:2500-20. [PMID: 11948165 PMCID: PMC134987 DOI: 10.1128/jb.184.9.2500-2520.2002] [Citation(s) in RCA: 246] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The stringent response in Bacillus subtilis was characterized by using proteome and transcriptome approaches. Comparison of protein synthesis patterns of wild-type and relA mutant cells cultivated under conditions which provoke the stringent response revealed significant differences. According to their altered synthesis patterns in response to DL-norvaline, proteins were assigned to four distinct classes: (i) negative stringent control, i.e., strongly decreased protein synthesis in the wild type but not in the relA mutant (e.g., r-proteins); (ii) positive stringent control, i.e., induction of protein synthesis in the wild type only (e.g., YvyD and LeuD); (iii) proteins that were induced independently of RelA (e.g., YjcI); and (iv) proteins downregulated independently of RelA (e.g., glycolytic enzymes). Transcriptome studies based on DNA macroarray techniques were used to complement the proteome data, resulting in comparable induction and repression patterns of almost all corresponding genes. However, a comparison of both approaches revealed that only a subset of RelA-dependent genes or proteins was detectable by proteomics, demonstrating that the transcriptome approach allows a more comprehensive global gene expression profile analysis. The present study presents the first comprehensive description of the stringent response of a bacterial species and an almost complete map of protein-encoding genes affected by (p)ppGpp. The negative stringent control concerns reactions typical of growth and reproduction (ribosome synthesis, DNA synthesis, cell wall synthesis, etc.). Negatively controlled unknown y-genes may also code for proteins with a specific function during growth and reproduction (e.g., YlaG). On the other hand, many genes are induced in a RelA-dependent manner, including genes coding for already-known and as-yet-unknown proteins. A passive model is preferred to explain this positive control relying on the redistribution of the RNA polymerase under the influence of (p)ppGpp.
Collapse
Affiliation(s)
- Christine Eymann
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, D-17487 Greifswald, Germany
| | | | | | | |
Collapse
|
18
|
Tedin K, Norel F. Comparison of DeltarelA strains of Escherichia coli and Salmonella enterica serovar Typhimurium suggests a role for ppGpp in attenuation regulation of branched-chain amino acid biosynthesis. J Bacteriol 2001; 183:6184-96. [PMID: 11591661 PMCID: PMC100096 DOI: 10.1128/jb.183.21.6184-6196.2001] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The growth recovery of Escherichia coli K-12 and Salmonella enterica serovar Typhimurium DeltarelA mutants were compared after nutritional downshifts requiring derepression of the branched-chain amino acid pathways. Because wild-type E. coli K-12 and S. enterica serovar Typhimurium LT2 strains are defective in the expression of the genes encoding the branch point acetohydroxy acid synthetase II (ilvGM) and III (ilvIH) isozymes, respectively, DeltarelA derivatives corrected for these mutations were also examined. Results indicate that reduced expression of the known global regulatory factors involved in branched-chain amino acid biosynthesis cannot completely explain the observed growth recovery defects of the DeltarelA strains. In the E. coli K-12 MG1655 DeltarelA background, correction of the preexisting rph-1 allele which causes pyrimidine limitations resulted in complete loss of growth recovery. S. enterica serovar Typhimurium LT2 DeltarelA strains were fully complemented by elevated basal ppGpp levels in an S. enterica serovar Typhimurium LT2 DeltarelA spoT1 mutant or in a strain harboring an RNA polymerase mutation conferring a reduced RNA chain elongation rate. The results are best explained by a dependence on the basal levels of ppGpp, which are determined by relA-dependent changes in tRNA synthesis resulting from amino acid starvations. Expression of the branched-chain amino acid operons is suggested to require changes in the RNA chain elongation rate of the RNA polymerase, which can be achieved either by elevation of the basal ppGpp levels or, in the case of the E. coli K-12 MG1655 strain, through pyrimidine limitations which partially compensate for reduced ppGpp levels. Roles for ppGpp in branched-chain amino acid biosynthesis are discussed in terms of effects on the synthesis of known global regulatory proteins and current models for the control of global RNA synthesis by ppGpp.
Collapse
Affiliation(s)
- K Tedin
- Unité de Génétique des Bactéries Intracellulaires, Institut Pasteur, F-75724 Paris Cedex 15, France.
| | | |
Collapse
|
19
|
Kim BH, Bang IS, Lee SY, Hong SK, Bang SH, Lee IS, Park YK. Expression of cspH, encoding the cold shock protein in Salmonella enterica serovar Typhimurium UK-1. J Bacteriol 2001; 183:5580-8. [PMID: 11544220 PMCID: PMC95449 DOI: 10.1128/jb.183.19.5580-5588.2001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Both Salmonella enterica serovar Typhimurium and Escherichia coli contain the cspH gene encoding CspH, one of the cold shock proteins (CSPs). In this study, we investigated the expression of cspH in S. enterica serovar Typhimurium and found that it was induced in response to a temperature downshift during exponential phase. The cspH promoter was activated at 37 degrees C, and its mRNA was more stable than the other csp mRNAs at 37 degrees C. Moreover, lacZ expression of the translational cspH-lacZ fusion was induced at that temperature. Interestingly, the cspH mRNA had a much shorter 5'-untranslated region than those in the other cold-shock-inducible genes, and the promoter sequence, which was only 55 bp, was sufficient for cspH expression. The 14-base downstream box located 12 bases downstream of the initiation codon of cspH mRNA was essential for its cold shock activation.
Collapse
Affiliation(s)
- B H Kim
- Graduate School of Biotechnology, Korea University, Seoul 136-701, Korea
| | | | | | | | | | | | | |
Collapse
|
20
|
Barker MM, Gaal T, Josaitis CA, Gourse RL. Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J Mol Biol 2001; 305:673-88. [PMID: 11162084 DOI: 10.1006/jmbi.2000.4327] [Citation(s) in RCA: 269] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To determine the role of ppGpp in both negative and positive regulation of transcription initiation during exponential growth in Escherichia coli, we examined transcription in vivo and in vitro from the growth-rate-dependent rRNA promoter rrnB P1 and from the inversely growth-rate-dependent amino acid biosynthesis/transport promoters PargI, PhisG, PlysC, PpheA, PthrABC, and PlivJ. rrnB P1 promoter activity was slightly higher at all growth-rates in strains unable to synthesize ppGpp (deltarelAdeltaspoT) than in wild-type strains. Consistent with this observation and with the large decrease in rRNA transcription during the stringent response (when ppGpp levels are much higher), ppGpp inhibited transcription from rrnB P1 in vitro. In contrast, amino acid promoter activity was considerably lower in deltarelAdeltaspoT strains than in wild-type strains, but ppGpp had no effect on amino acid promoter activity in vitro. Detailed kinetic analysis in vitro indicated that open complexes at amino acid promoters formed much more slowly and were much longer-lived than rrnB P1 open complexes. ppGpp did not increase the rates of association with, or escape from, amino acid promoters in vitro, consistent with its failure to stimulate transcription directly. In contrast, ppGpp decreased the half-lives of open complexes at all promoters, whether the half-life was seconds (rrnB P1) or hours (amino acid promoters). The results described here and in the accompanying paper indicate that ppGpp directly inhibits transcription, but only from promoters like rrnB P1 that make short-lived open complexes. The results indicate that stimulation of amino acid promoters occurs indirectly. The accompanying paper evaluates potential models for positive control of amino acid promoters by ppGpp that might explain the requirement of ppGpp for amino acid prototrophy.
Collapse
Affiliation(s)
- M M Barker
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, 53706, USA
| | | | | | | |
Collapse
|
21
|
Barker MM, Gaal T, Gourse RL. Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP. J Mol Biol 2001; 305:689-702. [PMID: 11162085 DOI: 10.1006/jmbi.2000.4328] [Citation(s) in RCA: 163] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Strains containing ppGpp, a nucleotide whose synthesis is dependent on the RelA and SpoT proteins of Escherichia coli, display slightly lower rRNA promoter activity and much higher amino acid biosynthesis/transport promoter activity than deltarelAdeltaspoT strains. In the accompanying paper, we show that ppGpp directly inhibits rRNA promoter activity in vitro by decreasing the lifetime of the rrn P1 open complex. However, ppGpp does not stimulate amino acid promoter activity in vitro. We show here that RNA polymerase (RNAP) mutants, selected to confer prototrophy to deltarelAdeltaspoT strains, mimic the effects of ppGpp on wild-type RNAP. Based on the positions of the mutant residues that confer prototrophy in the structure of core RNAP, we suggest molecular models for how the mutants, and by analogy ppGpp, generally decrease the lifetime of open complexes. We show that amino acid promoters require higher concentrations of RNAP for function in vitro and in vivo than control promoters, and are more sensitive to competition for RNAP in vivo than control promoters. Furthermore, we show that the requirement of an amino acid promoter for ppGpp in vivo can be alleviated by increasing its rate-limiting RNAP-binding step. Our data are consistent with a previously proposed passive model in which ppGpp inhibits stable RNA synthesis directly by reducing the lifetime of the rrn P1 open complex, liberating enough RNAP to stimulate transcription from amino acid promoters. Our data also place considerable constraints on models invoking hypothetical factors that might increase amino acid promoter activity in a ppGpp-dependent fashion.
Collapse
MESH Headings
- Amino Acids/biosynthesis
- Amino Acids/genetics
- Binding, Competitive
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Ribosomal/genetics
- DNA-Directed RNA Polymerases/chemistry
- DNA-Directed RNA Polymerases/genetics
- DNA-Directed RNA Polymerases/metabolism
- Escherichia coli/drug effects
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Gene Expression Regulation, Bacterial/drug effects
- Genes, Bacterial/genetics
- Guanosine Tetraphosphate/metabolism
- Guanosine Tetraphosphate/pharmacology
- Half-Life
- Kinetics
- Ligases/metabolism
- Models, Genetic
- Models, Molecular
- Mutation/genetics
- Nucleic Acid Denaturation/genetics
- Promoter Regions, Genetic/genetics
- Protein Conformation
- Protein Subunits
- Pyrophosphatases/metabolism
- RNA, Bacterial/biosynthesis
- RNA, Bacterial/genetics
- Transcription, Genetic/drug effects
Collapse
Affiliation(s)
- M M Barker
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, 53706, USA
| | | | | |
Collapse
|
22
|
Choy HE. The study of guanosine 5'-diphosphate 3'-diphosphate-mediated transcription regulation in vitro using a coupled transcription-translation system. J Biol Chem 2000; 275:6783-9. [PMID: 10702235 DOI: 10.1074/jbc.275.10.6783] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The effects of the "alarmone" guanosine 5'-diphosphate 3'-diphosphate (ppGpp) on regulation of the Salmonella typhimurium histindine operon and the Escherichia coli tRNA(leu) operon were analyzed in vitro using a DNA-dependent transcription-translation system, S-30. The expression of the hisG promoter is positively regulated by ppGpp, whereas that of the leuV promoter (of tRNA(1eu)) is negatively regulated by ppGpp. In an attempt to understand the global regulatory mechanism of ppGpp control, interrelationship between ppGpp-dependent activation and repression of gene expression was examined using these promoters as models. It has been traditionally supposed that the ppGpp-dependent regulation, at least for the activation, is by a passive mode of control: the activation of gene expression by ppGpp is a consequence of the repression of stable RNA gene expression in the condition of RNA polymerase limiting. To test this model, the ppGpp-dependent regulations of both an activable promoter (hisGp) and a repressible promoter (leuVp) were determined in vitro simultaneously using a mixed template setup. The rationale for this exercise was to see whether the ppGpp-dependent activation and repression are inversely correlated in the in vitro condition in which RNA polymerase is limiting. No correlation was observed. It was concluded that the ppGpp-dependent activation is independent of the repression. Moreover, it was proposed that ppGpp-dependent activation and repression are mediated by titratable factors, each of which operate independently.
Collapse
Affiliation(s)
- H E Choy
- Department of Biochemistry, Dankook University Medical College, Chungnam, Chonan, Anseo, San 29, Korea.
| |
Collapse
|
23
|
Kuhar I, Zgur-Bertok D. Transcription regulation of the colicin K cka gene reveals induction of colicin synthesis by differential responses to environmental signals. J Bacteriol 1999; 181:7373-80. [PMID: 10572143 PMCID: PMC103702 DOI: 10.1128/jb.181.23.7373-7380.1999] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Colicin-producing strains occur frequently in natural populations of Escherichia coli, and colicinogenicity seems to provide a competitive advantage in the natural habitat. A cka-lacZ fusion was used to study the regulation of expression of the colicin K structural gene. Expression is growth phase dependent, with high activity in the late stationary phase. Nutrient depletion induces the expression of cka due to an increase in ppGpp. Temperature is a strong signal for cka expression, since only basal-level activity was detected at 22 degrees C. Mitomycin C induction demonstrates that cka expression is regulated to a lesser extent by the SOS response independently of ppGpp. Increased osmolarity induces a partial increase, while the global regulator integration host factor inhibits expression in the late stationary phase. Induction of cka was demonstrated to be independent of the cyclic AMP-Crp complex, carbon source, RpoS, Lrp, H-NS, pH, and short-chain fatty acids. In contrast to colicin E1, cka expression is independent of catabolite repression and is partially affected by anaerobiosis only upon SOS induction. These results indicate that while different colicins are expressed in response to some common signals such as nutrient depletion, the expression of individual colicins could be further influenced by specific environmental cues.
Collapse
Affiliation(s)
- I Kuhar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000 Ljubljana, Slovenia
| | | |
Collapse
|
24
|
Wright BE, Longacre A, Reimers JM. Hypermutation in derepressed operons of Escherichia coli K12. Proc Natl Acad Sci U S A 1999; 96:5089-94. [PMID: 10220423 PMCID: PMC21821 DOI: 10.1073/pnas.96.9.5089] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This article presents evidence that starvation for leucine in an Escherichia coli auxotroph triggers metabolic activities that specifically target the leu operon for derepression, increased rates of transcription, and mutation. Derepression of the leu operon was a prerequisite for its activation by the signal nucleotide, guanosine tetraphosphate, which accumulates in response to nutritional stress (the stringent response). A quantitative correlation was established between leuB mRNA abundance and leuB- reversion rates. To further demonstrate that derepression increased mutation rates, the chromosomal leu operon was placed under the control of the inducible tac promoter. When the leu operon was induced by isopropyl-D-thiogalactoside, both leuB mRNA abundance and leuB- reversion rates increased. These investigations suggest that guanosine tetraphosphate may contribute as much as attenuation in regulating leu operon expression and that higher rates of mutation are specifically associated with the derepressed leu operon.
Collapse
Affiliation(s)
- B E Wright
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | | | | |
Collapse
|
25
|
Cases I, de Lorenzo V. Expression systems and physiological control of promoter activity in bacteria. Curr Opin Microbiol 1998; 1:303-10. [PMID: 10066491 DOI: 10.1016/s1369-5274(98)80034-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Promoter activity in vivo is not just dependent on the performance of the regulator/promoter pair which may predominantly control transcription initiation in response to a given signal, it also relies on overimposed mechanisms that connect the activity of individual promoters to the metabolic and energetic status of the bacterial cells. Such mechanisms - which frequently become limiting for biotechnological applications involving regulated promoters - include classic (i.e. cAMP/CRP-mediated) or alternative catabolite control checks, recruitment of protein intermediates of the phosphotransferase sugar transport system, coregulation through protein-induced DNA bending and the interplay of sigma factors during various growth stages.
Collapse
Affiliation(s)
- I Cases
- Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones, Cientificas Campus de Cantoblanco, 28049 Madrid, Spain
| | | |
Collapse
|