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Rashid FZM, Crémazy FGE, Hofmann A, Forrest D, Grainger DC, Heermann DW, Dame RT. The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli. Nat Commun 2023; 14:7478. [PMID: 37978176 PMCID: PMC10656529 DOI: 10.1038/s41467-023-43322-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
Nucleoid associated proteins (NAPs) maintain the architecture of bacterial chromosomes and regulate gene expression. Thus, their role as transcription factors may involve three-dimensional chromosome re-organisation. While this model is supported by in vitro studies, direct in vivo evidence is lacking. Here, we use RT-qPCR and 3C-qPCR to study the transcriptional and architectural profiles of the H-NS (histone-like nucleoid structuring protein)-regulated, osmoresponsive proVWX operon of Escherichia coli at different osmolarities and provide in vivo evidence for transcription regulation by NAP-mediated chromosome re-modelling in bacteria. By consolidating our in vivo investigations with earlier in vitro and in silico studies that provide mechanistic details of how H-NS re-models DNA in response to osmolarity, we report that activation of proVWX in response to a hyperosmotic shock involves the destabilization of H-NS-mediated bridges anchored between the proVWX downstream and upstream regulatory elements (DRE and URE), and between the DRE and ygaY that lies immediately downstream of proVWX. The re-establishment of these bridges upon adaptation to hyperosmolarity represses the operon. Our results also reveal additional structural features associated with changes in proVWX transcript levels such as the decompaction of local chromatin upstream of the operon, highlighting that further complexity underlies the regulation of this model operon. H-NS and H-NS-like proteins are wide-spread amongst bacteria, suggesting that chromosome re-modelling may be a typical feature of transcriptional control in bacteria.
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Affiliation(s)
- Fatema-Zahra M Rashid
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333CC, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, 2333CC, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, 2333CC, The Netherlands
| | - Frédéric G E Crémazy
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333CC, The Netherlands
- Laboratoire Infection et Inflammation, INSERM, UVSQ, Université Paris-Saclay, Versailles, 78180, France
| | - Andreas Hofmann
- Statistical Physics and Theoretical Biophysics, Heidelberg University, Heidelberg, D-69120, Germany
| | - David Forrest
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - David C Grainger
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Dieter W Heermann
- Statistical Physics and Theoretical Biophysics, Heidelberg University, Heidelberg, D-69120, Germany
| | - Remus T Dame
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333CC, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, 2333CC, The Netherlands.
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, 2333CC, The Netherlands.
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Álvarez A, Toledo H. The histone-like protein HU has a role in gene expression during the acid adaptation response in Helicobacter pylori. Helicobacter 2017; 22. [PMID: 28244177 DOI: 10.1111/hel.12381] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Gastritis, ulcers, and gastric malignancy have been linked to human gastric epithelial colonization by Helicobacter pylori. Characterization of the mechanisms by which H. pylori adapts to the human stomach environment is of crucial importance to understand H. pylori pathogenesis. MATERIAL AND METHODS In an effort to extend our knowledge of these mechanisms, we used proteomic analysis and qRT-PCR to characterize the role of the histone-like protein HU in the response of H. pylori to low pH. RESULTS Proteomic analysis revealed that genes involved in chemotaxis, oxidative stress, or metabolism are under control of the HU protein. Also, expression of the virulence factors Ggt and NapA is affected by the null mutation of hup gene both at neutral and acid pH, as evidenced by qRT-PCR analysis. CONCLUSIONS Those results showed that H. pylori gene expression is altered by shift to low pH, thus confirming that acid exposure leads to profound changes in genomic expression, and suggest that the HU protein is a regulator that may help the bacterium adapt to the acid stress. In accordance with previous reports, we found that the HU protein participates in gene expression regulation when the microorganism is exposed to acid stress. Such transcriptional regulation underlies protein accumulation in the H. pylori cell.
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Affiliation(s)
- Alhejandra Álvarez
- Laboratory of Molecular Microbiology, Department of Molecular and Cellular Biology, Faculty of Medicine, ICBM, University of Chile, Santiago, Chile
| | - Héctor Toledo
- Laboratory of Molecular Microbiology, Department of Molecular and Cellular Biology, Faculty of Medicine, ICBM, University of Chile, Santiago, Chile
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3
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Sharadamma N, Khan K, Kumar S, Patil KN, Hasnain SE, Muniyappa K. Synergy between the N-terminal and C-terminal domains of Mycobacterium tuberculosis HupB is essential for high-affinity binding, DNA supercoiling and inhibition of RecA-promoted strand exchange. FEBS J 2011; 278:3447-62. [PMID: 21787377 DOI: 10.1111/j.1742-4658.2011.08267.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The occurrence of DNA architectural proteins containing two functional domains derived from two different architectural proteins is an interesting emerging research theme in the field of nucleoid structure and function. Mycobacterium tuberculosis HupB, unlike Escherichia coli HU, is a two-domain protein that, in the N-terminal region, shows broad sequence homology with bacterial HU. The long C-terminal extension, on the other hand, contains seven PAKK/KAAK motifs, which are characteristic of the histone H1/H5 family of proteins. In this article, we describe several aspects of HupB function, in comparison with its truncated derivatives lacking either the C-terminus or N-terminus. We found that HupB binds a variety of DNA repair and replication intermediates with K(d) values in the nanomolar range. By contrast, the N-terminal fragment of M. tuberculosis HupB (HupB(MtbN)) showed diminished DNA-binding activity, with K(d) values in the micromolar range, and the C-terminal domain was completely devoid of DNA-binding activity. Unlike HupB(MtbN) , HupB was able to constrain DNA in negative supercoils and introduce negative superhelical turns into relaxed DNA. Similarly, HupB exerted a robust inhibitory effect on DNA strand exchange promoted by cognate and noncognate RecA proteins, whereas HupB(MtbN), even at a 50-fold molar excess, had no inhibitory effect. Considered together, these results suggest that synergy between the N-terminal and C-terminal domains of HupB is essential for its DNA-binding ability, and to modulate the topological features of DNA, which has implications for processes such as DNA compaction, gene regulation, homologous recombination, and DNA repair.
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Affiliation(s)
- N Sharadamma
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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Nir G, Lindner M, Dietrich HRC, Girshevitz O, Vorgias CE, Garini Y. HU protein induces incoherent DNA persistence length. Biophys J 2011; 100:784-790. [PMID: 21281594 DOI: 10.1016/j.bpj.2010.12.3687] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 11/24/2010] [Accepted: 12/02/2010] [Indexed: 11/29/2022] Open
Abstract
HU is a highly conserved protein that is believed to play an important role in the architecture and dynamic compaction of bacterial DNA. Its ability to control DNA bending is crucial for functions such as transcription and replication. The effects of HU on the DNA structure have been studied so far mainly by single molecule methods that require us to apply stretching forces on the DNA and therefore may perturb the DNA-protein interaction. To overcome this hurdle, we study the effect of HU on the DNA structure without applying external forces by using an improved tethered particle motion method. By combining the results with DNA curvature analysis from atomic force microscopy measurements we find that the DNA consists of two different curvature distributions and the measured persistence length is determined by their interplay. As a result, the effective persistence length adopts a bimodal property that depends primarily on the HU concentration. The results can be explained according to a recently suggested model that distinguishes single protein binding from cooperative protein binding.
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Affiliation(s)
- Guy Nir
- Physics Department, Bar Ilan University, Ramat-Gan, Israel; Institute for Nanotechnology, Bar Ilan University, Ramat-Gan, Israel
| | - Moshe Lindner
- Physics Department, Bar Ilan University, Ramat-Gan, Israel; Institute for Nanotechnology, Bar Ilan University, Ramat-Gan, Israel
| | - Heidelinde R C Dietrich
- Department of Imaging Science and Technology, Delft University of Technology, Delft, The Netherlands
| | - Olga Girshevitz
- Institute for Nanotechnology, Bar Ilan University, Ramat-Gan, Israel
| | - Constantinos E Vorgias
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Yuval Garini
- Physics Department, Bar Ilan University, Ramat-Gan, Israel; Institute for Nanotechnology, Bar Ilan University, Ramat-Gan, Israel.
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5
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Peng S, Tasara T, Hummerjohann J, Stephan R. An overview of molecular stress response mechanisms in Escherichia coli contributing to survival of Shiga toxin-producing Escherichia coli during raw milk cheese production. J Food Prot 2011; 74:849-64. [PMID: 21549061 DOI: 10.4315/0362-028x.jfp-10-469] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ability of foodborne pathogens to survive in certain foods mainly depends on stress response mechanisms. Insight into molecular properties enabling pathogenic bacteria to survive in food is valuable for improvement of the control of pathogens during food processing. Raw milk cheeses are a potential source for human infections with Shiga toxin-producing Escherichia coli (STEC). In this review, we focused on the stress response mechanisms important for allowing STEC to survive raw milk cheese production processes. The major components and regulation pathways for general, acid, osmotic, and heat shock stress responses in E. coli and the implications of these responses for the survival of STEC in raw milk cheeses are discussed.
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Affiliation(s)
- Silvio Peng
- Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstrasse 272, 8057 Zürich, Switzerland
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6
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Nguyen HH, de la Tour CB, Toueille M, Vannier F, Sommer S, Servant P. The essential histone-like protein HU plays a major role inDeinococcus radioduransnucleoid compaction. Mol Microbiol 2009; 73:240-52. [DOI: 10.1111/j.1365-2958.2009.06766.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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7
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Oberto J, Nabti S, Jooste V, Mignot H, Rouviere-Yaniv J. The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction. PLoS One 2009; 4:e4367. [PMID: 19194530 PMCID: PMC2634741 DOI: 10.1371/journal.pone.0004367] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 12/17/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The Escherichia coli heterodimeric HU protein is a small DNA-bending protein associated with the bacterial nucleoid. It can introduce negative supercoils into closed circular DNA in the presence of topoisomerase I. Cells lacking HU grow very poorly and display many phenotypes. METHODOLOGY/PRINCIPAL FINDINGS We analyzed the transcription profile of every Escherichia coli gene in the absence of one or both HU subunits. This genome-wide in silico transcriptomic approach, performed in parallel with in vivo genetic experimentation, defined the HU regulon. This large regulon, which comprises 8% of the genome, is composed of four biologically relevant gene classes whose regulation responds to anaerobiosis, acid stress, high osmolarity, and SOS induction. CONCLUSIONS/SIGNIFICANCE The regulation a large number of genes encoding enzymes involved in energy metabolism and catabolism pathways by HU explains the highly pleiotropic phenotype of HU-deficient cells. The uniform chromosomal distribution of the many operons regulated by HU strongly suggests that the transcriptional and nucleoid architectural functions of HU constitute two aspects of a unique protein-DNA interaction mechanism.
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Affiliation(s)
- Jacques Oberto
- Laboratoire de Physiologie Bactérienne, CNRS, UPR 9073, Institut de Biologie Physico-chimique, Paris, France
- * E-mail: (JO); (JR-Y)
| | - Sabrina Nabti
- Laboratoire de Physiologie Bactérienne, CNRS, UPR 9073, Institut de Biologie Physico-chimique, Paris, France
| | - Valérie Jooste
- INSERM, UMR 866, Epidemiology and Biostatistics group, University of Dijon, Dijon, France
| | | | - Josette Rouviere-Yaniv
- Laboratoire de Physiologie Bactérienne, CNRS, UPR 9073, Institut de Biologie Physico-chimique, Paris, France
- * E-mail: (JO); (JR-Y)
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8
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Stoebel DM, Free A, Dorman CJ. Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria. Microbiology (Reading) 2008; 154:2533-2545. [PMID: 18757787 DOI: 10.1099/mic.0.2008/020693-0] [Citation(s) in RCA: 206] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Daniel M. Stoebel
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin 2, Ireland
| | - Andrew Free
- Institute of Evolutionary Biology, University of Edinburgh, Room 714a, Darwin Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Charles J. Dorman
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin 2, Ireland
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9
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Ram EVSR, Naik R, Ganguli M, Habib S. DNA organization by the apicoplast-targeted bacterial histone-like protein of Plasmodium falciparum. Nucleic Acids Res 2008; 36:5061-73. [PMID: 18663012 PMCID: PMC2528193 DOI: 10.1093/nar/gkn483] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Apicomplexans, including the pathogens Plasmodium and Toxoplasma, carry a nonphotosynthetic plastid of secondary endosymbiotic origin called the apicoplast. The P. falciparum apicoplast contains a 35 kb, circular DNA genome with limited coding capacity that lacks genes encoding proteins for DNA organization and replication. We report identification of a nuclear-encoded bacterial histone-like protein (PfHU) involved in DNA compaction in the apicoplast. PfHU is associated with apicoplast DNA and is expressed throughout the parasite's intra-erythocytic cycle. The protein binds DNA in a sequence nonspecific manner with a minimum binding site length of ∼27 bp and a Kd of ∼63 nM and displays a preference for supercoiled DNA. PfHU is capable of condensing Escherichia coli nucleoids in vivo indicating its role in DNA compaction. The unique 42 aa C-terminal extension of PfHU influences its DNA condensation properties. In contrast to bacterial HUs that bend DNA, PfHU promotes concatenation of linear DNA and inhibits DNA circularization. Atomic Force Microscopic study of PfHU–DNA complexes shows protein concentration-dependent DNA stiffening, intermolecular bundling and formation of DNA bridges followed by assembly of condensed DNA networks. Our results provide the first functional characterization of an apicomplexan HU protein and provide additional evidence for red algal ancestry of the apicoplast.
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Affiliation(s)
- E V S Raghu Ram
- Division of Molecular and Structural Biology, Central Drug Research Institute, Lucknow-226 001, India
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10
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Liu D, Yumoto H, Murakami K, Hirota K, Ono T, Nagamune H, Kayama S, Matsuo T, Miyake Y. The essentiality and involvement of Streptococcus intermedius histone-like DNA-binding protein in bacterial viability and normal growth. Mol Microbiol 2008; 68:1268-82. [PMID: 18410499 DOI: 10.1111/j.1365-2958.2008.06232.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Streptococcus intermedius histone-like DNA-binding protein (Si-HLP) is a homodimeric protein and, conserved with Escherichia coli HU, a well-documented nucleoid-associated protein (NAP). In E. coli, HU plays important roles as both structural and regulatory factors, but it is not essential for E. coli viability. Streptococcal HLP has been found to bind host cells and induce cytokine production, but its physiological role remains poorly defined. In the present study, using gene insertion knockout and tetracycline-regulated antisense RNA expression techniques, we determined whether Si-HLP is essential for bacterial viability and normal growth in S. intermedius. The Si-HLP-downregulated S. intermedius strain showed alterations in its morphology and surface properties. Downregulation of Si-HLP led to an expanded nucleoid to fill the intracellular space. Transcription levels of several genes, including virulence-associated factors, were found to be activated or repressed in the antisense Si-hlp RNA-expressing strain by real-time PCR and reverse-transcription PCR. Collectively, these data suggest that Si-HLP serves as an essential NAP governing the nucleoid architecture and controlling the gene transcription profile in S. intermedius.
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Affiliation(s)
- Dali Liu
- Department of Microbiology, Institute of Health Biosciences, The University of Tokushima Graduate School, 3-18-15 Kumamoto-cho, Tokushima 770-8504, Japan
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11
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Kar S, Choi EJ, Guo F, Dimitriadis EK, Kotova SL, Adhya S. Right-handed DNA Supercoiling by an Octameric Form of Histone-like Protein HU. J Biol Chem 2006; 281:40144-53. [PMID: 17062578 DOI: 10.1074/jbc.m605576200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In bacteria, the contribution of global nucleoid organization in determining cellular transcription programs is unclear. Using a mutant form of the most abundant nucleoid-associated protein HU, HUalpha(E38K,V42L), we previously showed that nucleoid remodeling by the mutant protein re-organizes the global transcription pattern. Here, we demonstrate that, unlike the dimeric wild-type HU, HUalpha(E38K,V42L) is an octamer and wraps DNA around its surface. The formation of wrapped nucleoprotein complexes by HUalpha(E38K,V42L) leads to a high degree of DNA condensation. The DNA wrapping is right-handed, which restrains positive supercoils. In vivo, HUalpha(E38K,V42L) shows altered association and distribution patterns with the genetic loci whose transcription are differentially affected in the mutant strain.
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Affiliation(s)
- Sudeshna Kar
- Laboratory of Molecular Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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12
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Weerasinghe JP, Dong T, Schertzberg MR, Kirchhof MG, Sun Y, Schellhorn HE. Stationary phase expression of the arginine biosynthetic operon argCBH in Escherichia coli. BMC Microbiol 2006; 6:14. [PMID: 16504055 PMCID: PMC1413537 DOI: 10.1186/1471-2180-6-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Accepted: 02/22/2006] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Arginine biosynthesis in Escherichia coli is elevated in response to nutrient limitation, stress or arginine restriction. Though control of the pathway in response to arginine limitation is largely modulated by the ArgR repressor, other factors may be involved in increased stationary phase and stress expression. RESULTS In this study, we report that expression of the argCBH operon is induced in stationary phase cultures and is reduced in strains possessing a mutation in rpoS, which encodes an alternative sigma factor. Using strains carrying defined argR, and rpoS mutations, we evaluated the relative contributions of these two regulators to the expression of argH using operon-lacZ fusions. While ArgR was the main factor responsible for modulating expression of argCBH, RpoS was also required for full expression of this biosynthetic operon at low arginine concentrations (below 60 microM L-arginine), a level at which growth of an arginine auxotroph was limited by arginine. When the argCBH operon was fully de-repressed (arginine limited), levels of expression were only one third of those observed in deltaargR mutants, indicating that the argCBH operon is partially repressed by ArgR even in the absence of arginine. In addition, argCBH expression was 30-fold higher in deltaargR mutants relative to levels found in wild type, fully-repressed strains, and this expression was independent of RpoS. CONCLUSION The results of this study indicate that both derepression and positive control by RpoS are required for full control of arginine biosynthesis in stationary phase cultures of E. coli.
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Affiliation(s)
- Jeevaka P Weerasinghe
- McMaster University, Department of Biology, Life Sciences Building, Rm. 218, 1280 Main Street West, Hamilton, ON, Canada, L8S 4K1
| | - Tao Dong
- McMaster University, Department of Biology, Life Sciences Building, Rm. 218, 1280 Main Street West, Hamilton, ON, Canada, L8S 4K1
| | - Michael R Schertzberg
- McMaster University, Department of Biology, Life Sciences Building, Rm. 218, 1280 Main Street West, Hamilton, ON, Canada, L8S 4K1
| | - Mark G Kirchhof
- McMaster University, Department of Biology, Life Sciences Building, Rm. 218, 1280 Main Street West, Hamilton, ON, Canada, L8S 4K1
| | - Yuan Sun
- McMaster University, Department of Biology, Life Sciences Building, Rm. 218, 1280 Main Street West, Hamilton, ON, Canada, L8S 4K1
| | - Herb E Schellhorn
- McMaster University, Department of Biology, Life Sciences Building, Rm. 218, 1280 Main Street West, Hamilton, ON, Canada, L8S 4K1
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13
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Preobrajenskaya OV, Starodubova ES, Karpov VL, Rouviere-Yaniv J. Comparison of the Local Concentration of the HU Protein for Particular Regions of Genomic DNA in Escherichia coli Cells in Vivo. Mol Biol 2005. [DOI: 10.1007/s11008-005-0074-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Thanbichler M, Wang SC, Shapiro L. The bacterial nucleoid: A highly organized and dynamic structure. J Cell Biochem 2005; 96:506-21. [PMID: 15988757 DOI: 10.1002/jcb.20519] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent advances in bacterial cell biology have revealed unanticipated structural and functional complexity, reminiscent of eukaryotic cells. Particular progress has been made in understanding the structure, replication, and segregation of the bacterial chromosome. It emerged that multiple mechanisms cooperate to establish a dynamic assembly of supercoiled domains, which are stacked in consecutive order to adopt a defined higher-level organization. The position of genetic loci on the chromosome is thereby linearly correlated with their position in the cell. SMC complexes and histone-like proteins continuously remodel the nucleoid to reconcile chromatin compaction with DNA replication and gene regulation. Moreover, active transport processes ensure the efficient segregation of sister chromosomes and the faithful restoration of nucleoid organization while DNA replication and condensation are in progress.
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Affiliation(s)
- Martin Thanbichler
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305-5329, USA
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15
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Kelly A, Goldberg MD, Carroll RK, Danino V, Hinton JCD, Dorman CJ. A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium. Microbiology (Reading) 2004; 150:2037-2053. [PMID: 15256548 DOI: 10.1099/mic.0.27209-0] [Citation(s) in RCA: 165] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Fis is a key DNA-binding protein involved in nucleoid organization and modulation of many DNA transactions, including transcription in enteric bacteria. The regulon of genes whose expression is influenced by Fis inSalmonella entericaserovar Typhimurium (S. typhimurium) has been defined by DNA microarray analysis. These data suggest that Fis plays a central role in coordinating the expression of both metabolic and type III secretion factors. The genes that were most strongly up-regulated by Fis were those involved in virulence and located in the pathogenicity islands SPI-1, SPI-2, SPI-3 and SPI-5. Similarly, motility and flagellar genes required Fis for full expression. This was shown to be a direct effect as purified Fis protein bound to the promoter regions of representative flagella and SPI-2 genes. Genes contributing to aspects of metabolism known to assist the bacterium during survival in the mammalian gut were also Fis-regulated, usually negatively. This category included components of metabolic pathways for propanediol utilization, biotin synthesis, vitamin B12transport, fatty acids and acetate metabolism, as well as genes for the glyoxylate bypass of the tricarboxylic acid cycle. Genes found to be positively regulated by Fis included those for ethanolamine utilization. The data reported reveal the central role played by Fis in coordinating the expression of both housekeeping and virulence factors required byS. typhimuriumduring life in the gut lumen or during systemic infection of host cells.
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Affiliation(s)
- Arlene Kelly
- Department of Microbiology, Moyne Institute of Preventive Medicine, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Martin D Goldberg
- Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Ronan K Carroll
- Department of Microbiology, Moyne Institute of Preventive Medicine, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Vittoria Danino
- Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Jay C D Hinton
- Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, University of Dublin, Trinity College, Dublin 2, Ireland
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16
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Lee SJ, Gralla JD. Osmo-regulation of bacterial transcription via poised RNA polymerase. Mol Cell 2004; 14:153-62. [PMID: 15099515 DOI: 10.1016/s1097-2765(04)00202-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2003] [Revised: 02/27/2004] [Accepted: 03/08/2004] [Indexed: 11/30/2022]
Abstract
Adaptation to high-salt environments is critical for the survival of a wide range of cells, especially for pathogenic bacteria that colonize the animal gut and urinary tract. The adaptation strategy involves production of the salt potassium glutamate, which induces a specific gene expression program that produces electro-neutral osmolytes while inhibiting general sigma(70) transcription. These data show that in Escherichia coli potassium glutamate stimulates transcription by disengaging inhibitory polymerase interactions at a sigma(38) promoter. These occur in an upstream region that is marked by an osmotic shock promoter DNA consensus sequence. The disruption activates a poised RNA polymerase to transcribe. This transcription program leads to the production of osmolytes that are shown to have only minor effects on transcription and therefore help to restore normal cell function. An osmotic shock gene expression cycle is discussed.
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Affiliation(s)
- Shun Jin Lee
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, P.O. Box 951569, Los Angeles, CA 90095, USA
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17
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Abstract
The role of HU in Escherichia coli as both a protein involved in DNA compaction and as a protein with regulatory function seems to be firmly established. However, a critical look at the available data reveals that this is not true for each of the proposed roles of this protein. The role of HU as a regulatory or accessory protein in a number of systems has been thoroughly investigated and in many cases has been largely elucidated. However, almost 30 years after its discovery, convincing evidence for the proposed role of HU in DNA compaction is still lacking. Here we present an extensive literature survey of the available data which, in combination with novel microscopic insights, suggests that the role of HU could be the opposite as well. The protein is likely to play an architectural role, but instead of being responsible for DNA compaction it could be involved in antagonising compaction by other proteins such as H-NS.
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Affiliation(s)
- Remus Thei Dame
- Laboratory of Molecular Genetics, Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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18
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Kobayashi T, Takahara M, Miyagishima SY, Kuroiwa H, Sasaki N, Ohta N, Matsuzaki M, Kuroiwa T. Detection and localization of a chloroplast-encoded HU-like protein that organizes chloroplast nucleoids. THE PLANT CELL 2002; 14:1579-89. [PMID: 12119376 PMCID: PMC150708 DOI: 10.1105/tpc.002717] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2002] [Accepted: 03/27/2002] [Indexed: 05/19/2023]
Abstract
Chloroplast DNA (cpDNA) is packed into discrete structures called chloroplast nucleoids (cp-nucleoids). The structure of cpDNA is thought to be important for its maintenance and regulation. In bacteria and mitochondria, histone-like proteins (such as HU and Abf2, respectively) are abundant and play important roles in DNA organization. However, a primary structural protein has yet to be found in cp-nucleoids. Here, we identified an abundant DNA binding protein from isolated cp-nucleoids of the primitive red alga Cyanidioschyzon merolae. The purified protein had sequence homology with the bacterial histone-like protein HU, and it complemented HU-lacking Escherichia coli mutants. The protein, called HC (histone-like protein of chloroplast), was encoded by a single gene (CmhupA) in the C. merolae chloroplast genome. Using immunofluorescence and immunoelectron microscopy, we demonstrated that HC was distributed uniformly throughout the entire cp-nucleoid. The protein was expressed constitutively throughout the cell and the chloroplast division cycle, and it was able to condense DNA. These results indicate that HC, a bacteria-derived histone-like protein, primarily organizes cpDNA into the nucleoid.
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Affiliation(s)
- Tamaki Kobayashi
- Department of Biological Science, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan.
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19
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Rajkumari K, Gowrishankar J. An N-terminally truncated RpoS (sigma(S)) protein in Escherichia coli is active in vivo and exhibits normal environmental regulation even in the absence of rpoS transcriptional and translational control signals. J Bacteriol 2002; 184:3167-75. [PMID: 12029032 PMCID: PMC135099 DOI: 10.1128/jb.184.12.3167-3175.2002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RpoS (sigma(S)) in Escherichia coli is a stationary-phase-specific primary sigma factor of RNA polymerase which is 330 amino acids long and belongs to the eubacterial sigma(70) family of proteins. Conserved domain 1.1 at the N-terminal end of sigma(70) has been shown to be essential for RNA polymerase function, and its deletion has been shown to result in a dominant-lethal phenotype. We now report that a sigma(S) variant with a deletion of its N-terminal 50 amino acids (sigma(S)Delta1-50), when expressed in vivo either from a chromosomal rpoS::IS10 allele (in rho mutant strains) or from a plasmid-borne arabinose-inducible promoter, is as proficient as the wild type in directing transcription from the proU P1 promoter; at three other sigma(S)-dependent promoters that were tested (osmY, katE, and csiD), the truncated protein exhibited a three- to sevenfold reduced range of activities. Catabolite repression at the csiD promoter (which requires both sigma(S) and cyclic AMP [cAMP]-cAMP receptor protein for its activity) was also preserved in the strain expressing sigma(S)Delta1-50. The intracellular content of sigma(S)Delta1-50 was regulated by culture variables such as growth phase, osmolarity, and temperature in the same manner as that described earlier for sigma(S), even when the truncated protein was expressed from a template that possessed neither the transcriptional nor the translational control elements of wild-type rpoS. Our results indicate that, unlike that in sigma(70), the N-terminal domain in sigma(S) may not be essential for the protein to function as a sigma factor in vivo. Furthermore, our results suggest that the induction of sigma(S)-specific promoters in stationary phase and during growth under conditions of high osmolarity or low temperature is mediated primarily through the regulation of sigma(S) protein degradation.
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Affiliation(s)
- K Rajkumari
- Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
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20
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Sleator RD, Hill C. Bacterial osmoadaptation: the role of osmolytes in bacterial stress and virulence. FEMS Microbiol Rev 2002; 26:49-71. [PMID: 12007642 DOI: 10.1111/j.1574-6976.2002.tb00598.x] [Citation(s) in RCA: 480] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Two general strategies exist for the growth and survival of prokaryotes in environments of elevated osmolarity. The 'salt in cytoplasm' approach, which requires extensive structural modifications, is restricted mainly to members of the Halobacteriaceae. All other species have convergently evolved to cope with environments of elevated osmolarity by the accumulation of a restricted range of low molecular mass molecules, termed compatible solutes owing to their compatibility with cellular processes at high internal concentrations. Herein we review the molecular mechanisms governing the accumulation of these compounds, both in Gram-positive and Gram-negative bacteria, focusing specifically on the regulation of their transport/synthesis systems and the ability of these systems to sense and respond to changes in the osmolarity of the extracellular environment. Finally, we examine the current knowledge on the role of these osmostress responsive systems in contributing to the virulence potential of a number of pathogenic bacteria.
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Affiliation(s)
- Roy D Sleator
- Department of Microbiology and National Food Biotechnology Centre, University College Cork, Cork, Ireland
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21
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Rajkumari K, Gowrishankar J. In vivo expression from the RpoS-dependent P1 promoter of the osmotically regulated proU operon in Escherichia coli and Salmonella enterica serovar Typhimurium: activation by rho and hns mutations and by cold stress. J Bacteriol 2001; 183:6543-50. [PMID: 11673423 PMCID: PMC95484 DOI: 10.1128/jb.183.22.6543-6550.2001] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Unlike the sigma(70)-controlled P2 promoter for the osmotically regulated proU operon of Escherichia coli and Salmonella enterica serovar Typhimurium, the sigma(s)-controlled P1 promoter situated further upstream appears not to contribute to expression of the proU structural genes under ordinary growth conditions. For S. enterica proU P1, there is evidence that promoter crypticity is the result of a transcription attenuation phenomenon which is relieved by the deletion of a 22-base C-rich segment in the transcript. In this study, we have sought to identify growth conditions and trans-acting mutations which activate in vivo expression from proU P1. The cryptic S. enterica proU P1 promoter was activated, individually and additively, in a rho mutant (which is defective in the transcription termination factor Rho) as well as by growth at 10 degrees C. The E. coli proU P1 promoter was also cryptic in constructs that carried 1.2 kb of downstream proU sequence, and in these cases activation of in vivo expression was achieved either by a rho mutation during growth at 10 degrees C or by an hns null mutation (affecting the nucleoid protein H-NS) at 30 degrees C. The rho mutation had no effect at either 10 or 30 degrees C on in vivo expression from two other sigma(s)-controlled promoters tested, those for osmY and csiD. In cells lacking the RNA-binding regulator protein Hfq, induction of E. coli proU P1 at 10 degrees C and by hns mutation at 30 degrees C was still observed, although the hfq mutation was associated with a reduction in the absolute levels of P1 expression. Our results suggest that expression from proU P1 is modulated both by nucleoid structure and by Rho-mediated transcription attenuation and that this promoter may be physiologically important for proU operon expression during low-temperature growth.
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Affiliation(s)
- K Rajkumari
- Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
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22
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Abstract
In Gal repressosome assembly, a DNA loop is formed by the interaction of two GalR, bound to two distal operators, and the binding of the histone-like protein, HU, to an architecturally critical position on DNA to facilitate the GalR-GalR interaction. We show that GalR piggybacks HU to the critical position on the DNA through a specific GalR-HU interaction. This is the first example of HU making a specific contact with another protein. The GalR-HU contact that results in cooperative binding of the two proteins to DNA may be transient and absent in the final repressosome structure. A sequence-independent DNA-binding protein being recruited to an architectural site on DNA through a specific association with a regulatory protein may be a common mode for assembly of complex nucleoprotein structures.
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Affiliation(s)
- S Kar
- Department of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4255, USA
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23
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Elias AF, Bono JL, Carroll JA, Stewart P, Tilly K, Rosa P. Altered stationary-phase response in a Borrelia burgdorferi rpoS mutant. J Bacteriol 2000; 182:2909-18. [PMID: 10781562 PMCID: PMC102002 DOI: 10.1128/jb.182.10.2909-2918.2000] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The homolog of the chromosomally encoded stationary-phase sigma factor RpoS in Borrelia burgdorferi was inactivated using gyrB(r) as a selectable marker. Two-dimensional nonequilibrium pH gradient electrophoresis of stationary-phase cell lysates identified at least 11 differences between the protein profiles of the rpoS mutant and wild-type organisms. Wild-type B. burgdorferi had a growth phase-dependent resistance to 1 N NaCl, similar to the stationary-phase response reported for other bacteria. The B. burgdorferi rpoS mutant strain was less resistant to osmotic stress in stationary phase than the isogenic rpoS wild-type organism. The results indicate that the B. burgdorferi rpoS homolog influences protein composition and participates in stationary-phase-dependent osmotic resistance. This rpoS mutant will be useful for studying regulation of gene expression in response to changing environmental conditions.
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Affiliation(s)
- A F Elias
- Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, USA.
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24
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Jordi BJ, Higgins CF. The downstream regulatory element of the proU operon of Salmonella typhimurium inhibits open complex formation by RNA polymerase at a distance. J Biol Chem 2000; 275:12123-8. [PMID: 10766847 DOI: 10.1074/jbc.275.16.12123] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The intracellular concentration of K(+)-glutamate, chromatin-associated proteins, and a downstream regulatory element (DRE) overlapping with the coding sequence, have been implicated in the regulation of the proU operon of Salmonella typhimurium. The basal expression of the proU operon is low, but it is rapidly induced when the bacteria are grown in media of high osmolarity (e.g. 0.3 M NaCl). It has previously been suggested that increased intracellular concentrations of K(+)-glutamate activate the proU promoter in response to increased extracellular osmolarity. We show here that the activation of the proU promoter by K(+)-glutamate in vitro is nonspecific, and the in vivo regulation cannot simply be mimicked in vitro. In vivo specificity requires both the chromatin-associated protein H-NS and the DRE; they are both needed to maintain repression of proU expression at low osmolarity. How H-NS and the DRE repress the proU promoter in vivo has so far been unclear. We show that, in vivo, the DRE acts at a distance to inhibit open complex formation at the proU promoter.
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Affiliation(s)
- B J Jordi
- Department of Bacteriology, Institute of Infectious Diseases and Immunology, Faculty of Veterinary Sciences, Yalelaan 1, 3508 TD Utrecht, The Netherlands.
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25
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Cunning C, Elliott T. RpoS synthesis is growth rate regulated in Salmonella typhimurium, but its turnover is not dependent on acetyl phosphate synthesis or PTS function. J Bacteriol 1999; 181:4853-62. [PMID: 10438755 PMCID: PMC93972 DOI: 10.1128/jb.181.16.4853-4862.1999] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The RpoS sigma factor of enteric bacteria is either required for or augments the expression of a number of genes that are induced during nutrient limitation, growth into stationary phase, or in response to stresses, including high osmolarity. RpoS is regulated at multiple levels, including posttranscriptional control of its synthesis, protein turnover, and mechanisms that affect its activity directly. Here, the control of RpoS stability was investigated in Salmonella typhimurium by the isolation of a number of mutants specifically defective in RpoS turnover. These included 20 mutants defective in mviA, the ortholog of Escherichia coli rssB/sprE, and 13 mutants defective in either clpP or clpX which encode the protease active on RpoS. An hns mutant was also defective in RpoS turnover, thus confirming that S. typhimurium and E. coli have identical genetic requirements for this process. Some current models predict the existence of a kinase to phosphorylate the response regulator MviA, but no mutants affecting a kinase were recovered. An mviA mutant carrying the D58N substitution altering the predicted phosphorylation site is substantially defective, suggesting that phosphorylation of MviA on D58 is important for its function. No evidence was obtained to support models in which acetyl phosphate or the PTS system contributes to MviA phosphorylation. However, we did find a significant (fivefold) elevation of RpoS during exponential growth on acetate as the carbon and energy source. This behavior is due to growth rate-dependent regulation which increases RpoS synthesis at slower growth rates. Growth rate regulation operates at the level of RpoS synthesis and is mainly posttranscriptional but, surprisingly, is independent of hfq function.
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Affiliation(s)
- C Cunning
- Department of Microbiology and Immunology, West Virginia University Health Sciences Center, Morgantown, West Virginia 26506, USA
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26
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Antognoni F, Del Duca S, Kuraishi A, Kawabe E, Fukuchi-Shimogori T, Kashiwagi K, Igarashi K. Transcriptional inhibition of the operon for the spermidine uptake system by the substrate-binding protein PotD. J Biol Chem 1999; 274:1942-8. [PMID: 9890949 DOI: 10.1074/jbc.274.4.1942] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Inhibition of spermidine uptake in Escherichia coli, which occurs in the presence of accumulated polyamines, has been studied using the spermidine uptake operon consisting of the potA, -B, -C, and -D genes. Transcription of the potABCD operon was inhibited by PotD, a spermidine-binding protein usually found in the periplasm, and the inhibitory effect of PotD was increased by spermidine. Transcription was not affected by bovine serum albumin, PotA, or PotF, suggesting that the effects of PotD are specific to the PotD protein. In the presence of 8 mM spermidine, a 50% inhibition of transcription was observed with a molar ratio of approximately 1:500 of template DNA:PotD. It was found that PotD bound to regions -258 to -209 nucleotides upstream and +66 to +135 nucleotides downstream of the ATG initiation codon of the potA gene. Binding of PotD to the downstream site was stimulated by spermidine. Overexpression of PotD in Escherichia coli DH5alpha inhibited the uptake of spermidine, the synthesis of PotABCD mRNA, and expression of a lacZ reporter gene fused downstream of a potA gene containing the PotD binding sites. In cells overexpressing PotD, a large amount of PotD existed as PotD precursor in spheroplasts. Our results indicate that PotD precursor can also inhibit spermidine transport. The amino acid residues in PotD that are involved in its interaction with the potABCD operon were determined using mutated PotD proteins. Thr-35 and Ser-85 of PotD were found to be important for this interaction. These results suggest that transcription of the spermidine transport (potABCD) operon is inhibited in vivo by PotD precursor rather than PotD through its binding to two regions close to the transcriptional initiation site of the operon.
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Affiliation(s)
- F Antognoni
- Faculty of Pharmaceutical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
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27
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Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
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Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
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28
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Li S, Waters R. Escherichia coli strains lacking protein HU are UV sensitive due to a role for HU in homologous recombination. J Bacteriol 1998; 180:3750-6. [PMID: 9683467 PMCID: PMC107354 DOI: 10.1128/jb.180.15.3750-3756.1998] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
hupA and hupB encode the alpha and beta subunits of the Escherichia coli histone-like protein HU. Here we show that E. coli hup mutants are sensitive to UV in the rec+ sbc+, recBC sbcA, recBC sbcBC, umuDC, recF, and recD backgrounds. However, hupAB mutations do not enhance the UV sensitivity of resolvase-deficient recG ruvA strains. hupAB uvrA and hupAB recG strains are supersensitive to UV. hup mutations enhance the UV sensitivity of ruvA strains to a much lesser extent but enhance that of rus-1 ruvA strains to the same extent as for rus+ ruv+ strains. Our results suggest that HU plays a role in recombinational DNA repair that is not specifically limited to double-strand break repair or daughter strand gap repair; the lack of HU affects the RecG RusA and RuvABC pathways for Holliday junction processing equally if the two pathways are equally active in recombinational repair; the function of HU is not in the substrate processing step or in the RecFOR-directed synapsis action during recombinational repair. Furthermore, the UV sensitivity of hup mutants cannot be suppressed by overexpression of wild-type or mutant gyrB, which confers novobiocin resistance, or by different concentrations of a gyrase inhibitor that can increase or decrease the supercoiling of chromosomal DNA.
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Affiliation(s)
- S Li
- School of Biological Sciences, University of Wales Swansea, Swansea SA2 8PP, United Kingdom
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29
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Turner AK, Lovell MA, Hulme SD, Zhang-Barber L, Barrow PA. Identification of Salmonella typhimurium genes required for colonization of the chicken alimentary tract and for virulence in newly hatched chicks. Infect Immun 1998; 66:2099-106. [PMID: 9573095 PMCID: PMC108169 DOI: 10.1128/iai.66.5.2099-2106.1998] [Citation(s) in RCA: 125] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
From a collection of 2,800 Tn5-TC1 transposon mutants of Salmonella typhimurium F98, 18 that showed reduced intestinal colonization of 3-week-old chicks were identified. The sites of transposon insertion were determined for most of the mutants and included insertions in the lipopolysaccharide biosynthesis genes rfaK, rfaY, rfbK, and rfbB and the genes dksA, clpB, hupA, and sipC. In addition, identification was made of an insertion into a novel gene that encodes a protein showing similarity to the IIC component of the mannose class of phosphoenolpyruvate-carbohydrate phosphotransferase systems, which we putatively called ptsC. Transduction of most of the transposon mutations to a fresh S. typhimurium F98 genetic background and construction of defined mutations in the rfbK, dksA, hupA, sipC, and ptsC genes of S. typhimurium F98 supported the role in colonization of all but the pts locus. The virulence of the rfbK, dksA, hupA, sipC, and ptsC defined mutants and clpB and rfaY transductants in 1-day-old chicks was tested. All but the ptsC and rfaY mutants were attenuated for virulence. A number of other phenotypes associated with some of the mutations are described.
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Affiliation(s)
- A K Turner
- Institute for Animal Health, Compton, Near Newbury, Berkshire, United Kingdom
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30
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Afflerbach H, Schröder O, Wagner R. Effects of the Escherichia coli DNA-binding protein H-NS on rRNA synthesis in vivo. Mol Microbiol 1998; 28:641-53. [PMID: 9632265 DOI: 10.1046/j.1365-2958.1998.00829.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Escherichia coli DNA-binding protein H-NS is known to interact specifically with the upstream region of ribosomal RNA transcription units, where it causes transcriptional repression in vitro. Here, we present results demonstrating the effect of H-NS on rRNA transcription in vivo. rRNA synthesis rates were compared in cells that differ in the expression of functional H-NS or FIS molecules. We could show that in the absence of H-NS derepression of rRNA synthesis occurs at low growth rates. During the cell cycle H-NS is responsible for the rapid shut-off of rRNA synthesis at the end of the exponential phase. As it is known for FIS-dependent activation, the inhibitory function of H-NS is specific for P1, the first of the tandem rRNA promoters. The effect of H-NS on rRNA synthesis was further assessed under stress conditions. While under osmotic upshift the reduction in rRNA synthesis is clearly H-NS-dependent, no such influence could be detected at cold shock. Determination of the cellular ppGpp concentrations revealed that H-NS does not mediate its function via alterations in the synthesis of the global effector ppGpp.
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Affiliation(s)
- H Afflerbach
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
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31
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Rajkumari K, Ishihama A, Gowrishankar J. Evidence for transcription attenuation rendering cryptic a sigmaS-dependent promoter of the osmotically regulated proU operon of Salmonella typhimurium. J Bacteriol 1997; 179:7169-73. [PMID: 9371467 PMCID: PMC179661 DOI: 10.1128/jb.179.22.7169-7173.1997] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The osmotically regulated proU locus in Escherichia coli has two promoters, P1 and P2, that are recognized, respectively, by the sigmaS- and sigma70-bearing RNA polymerase holoenzymes. However, the equivalent of the P1 promoter does not appear to exist in Salmonella typhimurium. We demonstrate in this study that wild-type S. typhimurium has a cryptic P1 promoter that is recognized by sigmaS RNA polymerase in vitro and that a 22-bp deletion from +63 to +84 (relative to the start site of transcription) confers sigmaS-dependent in vivo expression of a reporter gene fusion to P1. Primer extension analysis of RNA isolated from cells carrying the wild-type and mutant S. typhimurium proU constructs indicated that a primer which hybridizes proximal to +60 is able to detect P1-initiated transcripts from both constructs but a primer which hybridizes distal to +85 is able to do so only from the latter. Our results suggest that the sigmaS-controlled proU P1 promoter in S. typhimurium may be rendered cryptic because of factor-dependent transcription attenuation within a short distance downstream of the promoter start site.
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Affiliation(s)
- K Rajkumari
- Centre for Cellular & Molecular Biology, Hyderabad, India
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32
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Louis P, Galinski EA. Characterization of genes for the biosynthesis of the compatible solute ectoine from Marinococcus halophilus and osmoregulated expression in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 4):1141-1149. [PMID: 9141677 DOI: 10.1099/00221287-143-4-1141] [Citation(s) in RCA: 168] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The genes of the biosynthetic pathway of ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) from the Gram-positive moderate halophile Marinococcus halophilus were cloned by functional expression in Escherichia coli. These genes were not only expressed, but also osmoregulated in E. coli, as demonstrated by increasing cytoplasmic ectoine concentration in response to medium salinity. Sequencing of a 4.4 kb fragment revealed four major ORFs, which were designated ectA, ectB, ectC and orfA. The significance of three of these genes for ectoine synthesis was proved by sequence comparison with known proteins and by physiological experiments. Several deletion derivatives of the sequenced fragment were introduced into E. coli and the resulting clones were investigated for their ability to synthesize ectoine or one of the intermediates in its biosynthetic pathway. It was demonstrated that ectA codes for L-2,4-diaminobutyric acid acetyltransferase, ectB for L-2,4-diaminobutyric acid transaminase and ectC for L-ectoine synthase. A DNA region upstream of ectA was shown to be necessary for the regulated expression of ectoine synthesis in response to the osmolarity of the medium.
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Affiliation(s)
- Petra Louis
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Erwin A Galinski
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
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33
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Free A, Dorman CJ. The Escherichia coli stpA gene is transiently expressed during growth in rich medium and is induced in minimal medium and by stress conditions. J Bacteriol 1997; 179:909-18. [PMID: 9006049 PMCID: PMC178776 DOI: 10.1128/jb.179.3.909-918.1997] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The transcriptional regulation of the stpA gene, encoding the Escherichia coli H-NS-like protein StpA, has been studied as a function of a variety of environmental conditions, and its response to trans-acting factors has been characterized. Chromosomally located stpA is expressed primarily from a promoter immediately upstream of the gene which is severely repressed by the homologous nucleoid-associated protein H-NS. However, we show here that even in a strain containing functional H-NS, stpA is transiently induced during growth of a batch culture in rich medium. It can also be induced strongly by osmotic shock and, to a lesser extent, by an increase in growth temperature. Moreover, when cells are grown in minimal medium, we observe a more sustained induction of stpA which is dependent on the leucine-responsive regulatory protein (Lrp). This enhanced level of stpA transcription is virtually abolished in an H-NS-independent manner when the culture undergoes carbon starvation. A sensitivity of the stpA promoter to DNA topology may contribute to some of these responses. Results reported here show that cloned fragments of the stpA promoter region can confer H-NS and Lrp responsiveness upon a lacZ reporter gene and suggest that several hundred base pairs of DNA upstream of the transcriptional start may be required for regulation by these two proteins.
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Affiliation(s)
- A Free
- Department of Microbiology, Trinity College, Dublin 2, Republic of Ireland.
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34
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Fang FC, Chen CY, Guiney DG, Xu Y. Identification of sigma S-regulated genes in Salmonella typhimurium: complementary regulatory interactions between sigma S and cyclic AMP receptor protein. J Bacteriol 1996; 178:5112-20. [PMID: 8752327 PMCID: PMC178306 DOI: 10.1128/jb.178.17.5112-5120.1996] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
sigma S (RpoS)-regulated lacZ transcriptional fusions in Salmonella typhimurium were identified from a MudJ transposon library by placing the rpoS gene under the control of the araBAD promoter and detecting lacZ expression in the presence or absence of arabinose supplementation. Western blot (immunoblot) analysis of bacteria carrying PBAD::rpoS demonstrated arabinose-dependent rpoS expression during all phases of growth. sigma S-dependent gene expression of individual gene fusions was confirmed by P22-mediated transduction of the MudJ insertions into wild-type or rpoS backgrounds. Analysis of six insertions revealed the known sigma S-regulated gene otsA, as well as five novel loci. Each of these genes is maximally expressed in stationary phase, and all but one show evidence of cyclic AMP receptor protein-dependent repression during logarithmic growth which is relieved in stationary phase. For these genes, as well as for the sigma S-regulated spvB plasmid virulence gene, a combination of rpoS overexpression and crp inactivation can result in high-level expression during logarithmic growth. The approach used to identify sigma S-regulated genes in this study provides a general method for the identification of genes controlled by trans-acting regulatory factors.
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Affiliation(s)
- F C Fang
- Department of Medicine, University of Colorado Health Sciences Center, Denver 80262, USA
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35
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Rajkumari K, Kusano S, Ishihama A, Mizuno T, Gowrishankar J. Effects of H-NS and potassium glutamate on sigmaS- and sigma70-directed transcription in vitro from osmotically regulated P1 and P2 promoters of proU in Escherichia coli. J Bacteriol 1996; 178:4176-81. [PMID: 8763946 PMCID: PMC178175 DOI: 10.1128/jb.178.14.4176-4181.1996] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We have used supercoiled DNA templates in this study to demonstrate that transcription in vitro from the P1 and P2 promoters of the osmoresponsive proU operon of Escherichia coli is preferentially mediated by the sigma(s) and sigma70-bearing RNA polymerase holoenzymes, respectively. Addition of potassium glutamate resulted in the activation of transcription from both P1 and P2 and also led to a pronounced enhancement of sigma(s) selectivity at the P1 promoter. Transcription from P2, and to a lesser extent from P1, was inhibited by the nucleoid protein H-NS but only in the absence of potassium glutamate. This study validates the existence of dual promoters with dual specificities for proU transcription. Our results also support the proposals that potassium, which is known to accumulate in cells grown at high osmolarity, is at least partially responsible for effecting the in vivo induction of proU transcription and that it does so through two mechanisms, directly by the activation of RNA polymerase and indirectly by the relief of repression imposed by H-NS.
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Affiliation(s)
- K Rajkumari
- Centre for Cellular & Molecular Biology, Hyderabad, India
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36
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Gowrishankar J, Manna D. How is osmotic regulation of transcription of the Escherichia coli proU operon achieved? A review and a model. Genetica 1996; 97:363-78. [PMID: 9081863 DOI: 10.1007/bf00055322] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The proU operon in enterobacteria encodes a binding-protein-dependent transporter for the active uptake of glycine betaine and L-proline, and serves an adaptive role during growth of cells in hyperosmolar environments. Transcription of proU is induced 400-fold under these conditions, but the underlying signal transduction mechanisms are incompletely understood. Increased DNA supercoiling and activation by potassium glutamate have each been proposed in alternative models as mediators of proU osmoresponsivity. We review here the available experimental data on proU regulation, and in particular the roles for DNA supercoiling, potassium glutamate, histone-like proteins of the bacterial nucleoid, and alternative sigma factors of RNA polymerase in such regulation. We also propose a new unifying model, in which the pronounced osmotic regulation of proU expression is achieved through the additive effects of at least three separate mechanisms, each comprised of a cis element [two promoters P1 and P2, and negative-regulatory-element (NRE) downstream of both promoters] and distinct trans-acting factors that interact with it: stationary-phase sigma factor RpoS with P1, nucleoid proteins HU and IHF with P2, and nucleoid protein H-NS with the NRE. In this model, potassium glutamate may activate proU expression through each of the three mechanisms whereas DNA supercoiling has a very limited role, if any, in the osmotic induction of proU transcription. We also suggest that proU may be a virulence gene in the pathogenic enterobacteria.
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Affiliation(s)
- J Gowrishankar
- Centre for Cellular and Molecular Biology, Hyderabad, India
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37
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Wise A, Brems R, Ramakrishnan V, Villarejo M. Sequences in the -35 region of Escherichia coli rpoS-dependent genes promote transcription by E sigma S. J Bacteriol 1996; 178:2785-93. [PMID: 8631665 PMCID: PMC178012 DOI: 10.1128/jb.178.10.2785-2793.1996] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
sigma S is an alternate sigma factor which functions with RNA polymerase to activate transcription of genes that are involved in a number of stress responses, including stationary-phase survival and osmoprotection. The similarity of the sigma S protein to sigma D (Escherichia coli's major sigma factor) in the regions thought to recognize and bind promoter sequences suggests that sigma S- and sigma D-associated RNA polymerases recognize promoter DNA in a similar manner. However, no promoter recognition sequence for sigma S holoenzyme (E sigma S) has been identified. An apparent conservation of cytosine nucleotides was noted in the -35 region of several sigma S-dependent promoters. Site-directed mutagenesis and reporter gene fusions were used to investigate the importance of the -35 cytosine nucleotides for sigma S-dependent transcription. Substitution of cytosine nucleotides for thymidine at the -35 site of the sigma D-dependent proU promoter effectively abolished transcription by E sigma D but allowed E sigma S to direct transcription from the mutant promoter. Inclusion of the sigma D consensus -10 hexamer strengthened transcription by E sigma S, demonstrating that both E sigma D and E sigma S can recognize the same -10 sequences. Conversely, replacement of -35 site cytosine nucleotides with thymidine in the sigma S-dependent osmY promoter reduced transcription by E sigma S and increased transcription by E sigma D. Our data suggest that DNA sequences in the -35 region function as part of a discriminator mechanism to shift transcription between E sigma D and E sigma S.
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Affiliation(s)
- A Wise
- Section of Microbiology, University of California, Davis 95616, USA.
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38
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Notley L, Ferenci T. Induction of RpoS-dependent functions in glucose-limited continuous culture: what level of nutrient limitation induces the stationary phase of Escherichia coli? J Bacteriol 1996; 178:1465-8. [PMID: 8631726 PMCID: PMC177823 DOI: 10.1128/jb.178.5.1465-1468.1996] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
treA and osmY expression and RpoS protein levels were investigated in glucose-limited continuous culture. The level of induction of these stationary-phase markers became as high during growth at a D of 0.1 to 0.2 h(-1) as in carbon-starved batch cultures but only in rpoS+ bacteria. The stress protectant trehalose was actually produced at higher levels at low growth rates than in stationary-phase cultures. The pattern of induction of RpoS-dependent activities could be separated from those regulated by cyclic AMP (cAMP) or endoinduction, and the induction occurred at extreme glucose limitation. Escherichia coli turns to a protective stationary-phase response when nutrient levels fall below approximately 10(-7) M glucose, which is insufficient to saturate scavenger transporters regulated by cAMP plus endoinducers, and this response is optimally expressed at 10(-6) M glucose. The high-level induction of protective functions also explains the maintenance energy requirement of bacterial growth at low dilution rates.
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Affiliation(s)
- L Notley
- Department of Microbiology, University of Sydney, New South Wales, Australia
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39
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Lamark T, Røkenes TP, McDougall J, Strøm AR. The complex bet promoters of Escherichia coli: regulation by oxygen (ArcA), choline (BetI), and osmotic stress. J Bacteriol 1996; 178:1655-62. [PMID: 8626294 PMCID: PMC177851 DOI: 10.1128/jb.178.6.1655-1662.1996] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The bet regulon allows Escherichia coli to synthesize the osmoprotectant glycine betaine from choline. It comprises a regulatory gene, betI, and three structural genes: betT (choline porter), betA (choline dehydrogenase), and betB (betaine aldehyde dehydrogenase). The bet genes are regulated by oxygen, choline, and osmotic stress. Primer extension analysis identified two partially overlapping promoters which were responsible for the divergent expression of the betT and betIBA transcripts. The transcripts were initiated 61 bp apart. Regulation of the promoters was investigated by using cat (chloramphenicol acetyltransferase) and lacZ (beta-galactosidase) operon fusions. Mutation of betI on plasmid F'2 revealed that BetI is a repressor which regulates both promoters simultaneously in response to the inducer choline. Both promoters remained inducible by osmotic stress in a betI mutant background. On the basis of experiments with hns and hns rpoS mutants, we conclude that osmoregulation of the bet promoters was hns independent. The bet promoters were repressed by ArcA under anaerobic growth conditions. An 89-bp promoter fragment, as well as all larger fragments tested, which included both transcriptional start points, displayed osmotic induction and BetI-dependent choline regulation when linked with a cat reporter gene on plasmid pKK232-8. Flanking DNA, presumably on the betT side of the promoter region, appeared to be needed for ArcA-dependent regulation of both promoters.
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Affiliation(s)
- T Lamark
- The Norwegian College of Fishery Science, University of Tromsø, Norway
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40
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Xu J, Johnson RC. Fis activates the RpoS-dependent stationary-phase expression of proP in Escherichia coli. J Bacteriol 1995; 177:5222-31. [PMID: 7545153 PMCID: PMC177312 DOI: 10.1128/jb.177.18.5222-5231.1995] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Fis is a general nucleoid-associated protein in Escherichia coli whose expression is highly regulated with respect to growth conditions. A random collection of transposon-induced lac fusions was screened for those which give increased expression in the presence of Fis in order to isolate a ProP-LacZ protein fusion. We find that proP, which encodes a low-affinity transporter of the important osmoprotectants proline and glycine betaine, is transcribed from two promoters. proP1 is transiently induced upon subculture and is upregulated by increases in medium osmolarity. As cells enter stationary phase, a second promoter, proP2, is strongly induced. This promoter can also be induced by high medium osmolarity in exponential phase. The activity of proP2 depends on Fis and the stationary-phase sigma factor sigmas. In the presence of Fis, proP2 expression is increased over 50-fold, as judged by the LacZ activity of cells carrying the proP-lacZ fusion as well as by direct RNA analysis, making this the most strongly activated promoter by Fis that has been described. Two Fis binding sites centered at positions -41 (site I) and -81 (site II) with respect to the transcription initiation site of P2 have been defined by DNase I footprinting. Mutations in site I largely abolish stationary-phase activation, while mutations at site II have a minor effect, suggesting that direct binding of Fis to site I is important for Fis-mediated activation of this promoter. In addition to Fis and sigmas, sequences located over 108 bp upstream of the proP2 transcription initiation site are required for efficient expression.
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Affiliation(s)
- J Xu
- Department of Biological Chemistry, UCLA School of Medicine 90095, USA
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41
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Fletcher SA, Csonka LN. Fine-structure deletion analysis of the transcriptional silencer of the proU operon of Salmonella typhimurium. J Bacteriol 1995; 177:4508-13. [PMID: 7635833 PMCID: PMC177203 DOI: 10.1128/jb.177.15.4508-4513.1995] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Transcriptional control of the osmotically regulated proU operon of Salmonella typhimurium is mediated in part by a transcriptional silencer downstream from the promoter (D.G. Overdier and L.N. Csonka, Proc. Natl. Acad. Sci. USA 89:3140-3144, 1992). We carried out a fine-structure deletion analysis to determine the structure and the position of the silencer, which demonstrated that this regulatory element is located between nucleotide positions +73 to +274 downstream from the transcription start site. The silencer appears to be made up of a number of components which have cumulative negative regulatory effects. Deletions or insertions of short nucleotide sequences (< 40 bp) between the proU promoter and the silencer do not disrupt repression exerted by the silencer, but long insertions (> or = 0.8 kbp) result in a high level of expression from the proU promoter, similar to that imparted by deletion of the entire silencer. The general DNA-binding protein H-NS is required for the full range of repression of the proU operon in media of low osmolality. Although in the presence of the silencer hns mutations increased basal expression from the proU promoter three- to sixfold, in the absence of the silencer they did not result in a substantial increase in basal expression from the proU promoter. Furthermore, deletion of the silencer in hns+ background was up to 10-fold more effective in increasing basal expression from the proU promoter than the hns mutations. These results indicate that osmotic control of the proU operon is dependent of some factor besides H-NS. We propose that the transcriptional regulation of this operon is effected in media of low osmolality by a protein which makes the promoter inaccessible to RNA polymerase by forming a complex containing the proU promoter and silencer.
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Affiliation(s)
- S A Fletcher
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA
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42
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Cam K, Cuzange A, Bouché JP. Sigma S-dependent overexpression of ftsZ in an Escherichia coli K-12 rpoB mutant that is resistant to the division inhibitors DicB and DicF RNA. MOLECULAR & GENERAL GENETICS : MGG 1995; 248:190-4. [PMID: 7651342 DOI: 10.1007/bf02190800] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The Escherichia coli genes dicF and dicB encode division inhibitors, which prevent the synthesis and activity, respectively, of the essential division protein FtsZ. A mutation at the C-terminal end of the RNA polymerase beta subunit renders cells resistant to both inhibitors. In the mutant strain the level of the ftsZ gene product is higher than in the wild type. Disruption of rpoS, which encodes the stationary phase sigma factor sigma S, lowers FtsZ protein levels in the mutant, and partially restores sensitivity to the inhibitors.
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Affiliation(s)
- K Cam
- Laboratoire de Microbiologie et Génétique moléculaire, Centre National de la Recherche Scientifique, Toulouse, France
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43
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Kempf B, Bremer E. OpuA, an osmotically regulated binding protein-dependent transport system for the osmoprotectant glycine betaine in Bacillus subtilis. J Biol Chem 1995; 270:16701-13. [PMID: 7622480 DOI: 10.1074/jbc.270.28.16701] [Citation(s) in RCA: 148] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Exogenously provided glycine betaine can efficiently protect Bacillus subtilis from the detrimental effects of high osmolarity environments. Through functional complementation of an Escherichia coli mutant deficient in glycine betaine uptake with a gene library from B. subtilis, we have identified a multicomponent glycine betaine transport system, OpuA. Uptake of radiolabeled glycine betaine in B. subtilis was found to be osmotically stimulated and was strongly decreased in a mutant strain lacking the OpuA transport system. DNA sequence analysis revealed that the components of the OpuA system are encoded by anoperon (opuA) comprising three structural genes: opuAA, opuAB, and opuAC. The products of these genes exhibit features characteristic for binding protein-dependent transport systems and in particular show homology to the glycine betaine uptake system ProU from E. coli. Expression of the opuA operon is under osmotic control. The transcriptional initiation sites of opuA were mapped by high resolution primer extension analysis, and two opuA mRNAs were detected that differed by 38 base pairs at their 5' ends. Synthesis of the shorter transcript was strongly increased in cells grown at high osmolarity, whereas the amount of the longer transcript did not vary in response to medium osmolarity. Physical and genetic mapping experiments allowed the positioning the opuA operon at 25 degrees on the genetic map of B. subtilis.
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Affiliation(s)
- B Kempf
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
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44
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Ding Q, Kusano S, Villarejo M, Ishihama A. Promoter selectivity control of Escherichia coli RNA polymerase by ionic strength: differential recognition of osmoregulated promoters by E sigma D and E sigma S holoenzymes. Mol Microbiol 1995; 16:649-56. [PMID: 7476160 DOI: 10.1111/j.1365-2958.1995.tb02427.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Transcription in vitro of two osmoregulated promoters, for the Escherichia coli osmB and osmY genes, was analysed using two species of RNA polymerase holoenzyme reconstituted from purified core enzyme and either sigma D (sigma 70, the major sigma in exponentially growing cells) or sigma S (sigma 38, the principal sigma at stationary growth phase). Under conditions of low ionic strength, the osmB and osmY promoters were transcribed by both E sigma D and E sigma S. Addition of up to 400 mM potassium glutamate (K glutamate), mimicking the intracellular ionic conditions under hyperosmotic stress, specifically enhanced transcription at these promoters by E sigma S but inhibited that by E sigma D. At similar high concentrations of potassium chloride (KCl), however, initiation at both these promoters was virtually undetectable. These data suggest that the RNA polymerase, E sigma S, itself can sense osmotic stress by responding to changes in intracellular K glutamate concentrations and altering its promoter selectivity in order to recognize certain osmoregulated promoters.
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Affiliation(s)
- Q Ding
- Department of Molecular Genetics, National Institute of Genetics, Shizuoka, Japan
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