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Verma SC, Harned A, Narayan K, Adhya S. Non-specific and specific DNA binding modes of bacterial histone, HU, separately regulate distinct physiological processes through different mechanisms. Mol Microbiol 2023; 119:439-455. [PMID: 36708073 PMCID: PMC10120378 DOI: 10.1111/mmi.15033] [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: 06/21/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 01/29/2023]
Abstract
The histone-like protein HU plays a diverse role in bacterial physiology from the maintenance of chromosome structure to the regulation of gene transcription. HU binds DNA in a sequence-non-specific manner via two distinct binding modes: (i) random binding to any DNA through ionic bonds between surface-exposed lysine residues (K3, K18, and K83) and phosphate backbone (non-specific); (ii) preferential binding to contorted DNA of given structures containing a pair of kinks (structure-specific) through conserved proline residues (P63) that induce and/or stabilize the kinks. First, we show here that the P63-mediated structure-specific binding also requires the three lysine residues, which are needed for a non-specific binding. Second, we demonstrate that substituting P63 to alanine in HU had no impact on non-specific binding but caused differential transcription of diverse genes previously shown to be regulated by HU, such as those associated with the organonitrogen compound biosynthetic process, galactose metabolism, ribosome biogenesis, and cell adhesion. The structure-specific binding also helps create DNA supercoiling, which, in turn, may influence directly or indirectly the transcription of other genes. Our previous and current studies show that non-specific and structure-specific HU binding appear to have separate functions- nucleoid architecture and transcription regulation- which may be true in other DNA-binding proteins.
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Affiliation(s)
- Subhash C Verma
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Adam Harned
- Center for Molecular Microscopy, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Kedar Narayan
- Center for Molecular Microscopy, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Sankar Adhya
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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Failure of Translation Initiation of the Next Gene Decouples Transcription at Intercistronic Sites and the Resultant mRNA Generation. mBio 2022; 13:e0128722. [PMID: 35695461 PMCID: PMC9239205 DOI: 10.1128/mbio.01287-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Escherichia coli, transcription is coupled with translation. The polar gal operon is transcribed galE-galT-galK-galM; however, about 10% of transcription terminates at the end of galE because of Rho-dependent termination (RDT). When galE translation is complete, galT translation should begin immediately. It is unclear whether RDT at the end of galE is due to decoupling of translation termination and transcription at the cistron junction. In this study, we show that RDT at the galE/galT cistron junction is linked to the failure of translation initiation at the start of galT, rather than translation termination at the end of galE. We also show that transcription pauses 130 nucleotides downstream from the site of galE translation termination, and this pause is required for RDT. IMPORTANCE Transcription of operons is initiated at the promoter of the first gene in the operon, continues through cistron junctions, and terminates at the end of the operon, generating a full-length mRNA. Here, we show that Rho-dependent termination of transcription occurs stochastically at a cistron junction, generating a stable mRNA that is shorter than the full-length mRNA. We further show that stochastic failure in translation initiation of the next gene, rather than the failure of translation termination of the preceding gene, causes the Rho-dependent termination. Thus, stochastic failure in translation initiation at the cistron junction causes the promoter-proximal gene to be transcribed more than promoter-distal genes within the operon.
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3
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Molecular Mechanisms of Transcription Initiation at gal Promoters and their Multi-Level Regulation by GalR, CRP and DNA Loop. Biomolecules 2015; 5:2782-807. [PMID: 26501343 PMCID: PMC4693257 DOI: 10.3390/biom5042782] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 09/25/2015] [Indexed: 11/16/2022] Open
Abstract
Studying the regulation of transcription of the gal operon that encodes the amphibolic pathway of d-galactose metabolism in Escherichia coli discerned a plethora of principles that operate in prokaryotic gene regulatory processes. In this chapter, we have reviewed some of the more recent findings in gal that continues to reveal unexpected but important mechanistic details. Since the operon is transcribed from two overlapping promoters, P1 and P2, regulated by common regulatory factors, each genetic or biochemical experiment allowed simultaneous discernment of two promoters. Recent studies range from genetic, biochemical through biophysical experiments providing explanations at physiological, mechanistic and single molecule levels. The salient observations highlighted here are: the axiom of determining transcription start points, discovery of a new promoter element different from the known ones that influences promoter strength, occurrence of an intrinsic DNA sequence element that overrides the transcription elongation pause created by a DNA-bound protein roadblock, first observation of a DNA loop and determination its trajectory, and piggybacking proteins and delivering to their DNA target.
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Effects of Four Different Regulatory Mechanisms on the Dynamics of Gene Regulatory Cascades. Sci Rep 2015; 5:12186. [PMID: 26184971 PMCID: PMC4505322 DOI: 10.1038/srep12186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 05/27/2015] [Indexed: 11/24/2022] Open
Abstract
Gene regulatory cascades (GRCs) are common motifs in cellular molecular networks. A given logical function in these cascades, such as the repression of the activity of a transcription factor, can be implemented by a number of different regulatory mechanisms. The potential consequences for the dynamic performance of the GRC of choosing one mechanism over another have not been analysed systematically. Here, we report the construction of a synthetic GRC in Escherichia coli, which allows us for the first time to directly compare and contrast the dynamics of four different regulatory mechanisms, affecting the transcription, translation, stability, or activity of a transcriptional repressor. We developed a biologically motivated mathematical model which is sufficient to reproduce the response dynamics determined by experimental measurements. Using the model, we explored the potential response dynamics that the constructed GRC can perform. We conclude that dynamic differences between regulatory mechanisms at an individual step in a GRC are often concealed in the overall performance of the GRC, and suggest that the presence of a given regulatory mechanism in a certain network environment does not necessarily mean that it represents a single optimal evolutionary solution.
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5
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Differential role of base pairs on gal promoters strength. J Mol Biol 2014; 427:792-806. [PMID: 25543084 DOI: 10.1016/j.jmb.2014.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 12/16/2014] [Accepted: 12/18/2015] [Indexed: 11/23/2022]
Abstract
Sequence alignments of promoters in prokaryotes postulated that the frequency of occurrence of a base pair at a given position of promoter elements reflects its contribution to intrinsic promoter strength. We directly assessed the contribution of the four base pairs in each position in the intrinsic promoter strength by keeping the context constant in Escherichia coli cAMP-CRP (cAMP receptor protein) regulated gal promoters by in vitro transcription assays. First, we show that base pair frequency within known consensus elements correlates well with promoter strength. Second, we observe some substitutions upstream of the ex-10 TG motif that are important for promoter function. Although the galP1 and P2 promoters overlap, only three positions where substitutions inactivated both promoters were found. We propose that RNA polymerase binds to the -12T base pair as part of double-stranded DNA while opening base pairs from -11A to +3 to form the single-stranded transcription bubble DNA during isomerization. The cAMP-CRP complex rescued some deleterious substitutions in the promoter region. The base pair roles and their flexibilities reported here for E. coli gal promoters may help construction of synthetic promoters in gene circuitry experiments in which overlapping promoters with differential controls may be warranted.
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Semsey S, Jauffred L, Csiszovszki Z, Erdőssy J, Stéger V, Hansen S, Krishna S. The effect of LacI autoregulation on the performance of the lactose utilization system in Escherichia coli. Nucleic Acids Res 2013; 41:6381-90. [PMID: 23658223 PMCID: PMC3711431 DOI: 10.1093/nar/gkt351] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The lactose operon of Escherichia coli is a paradigm system for quantitative understanding of gene regulation in prokaryotes. Yet, none of the many mathematical models built so far to study the dynamics of this system considered the fact that the Lac repressor regulates its own transcription by forming a transcriptional roadblock at the O3 operator site. Here we study the effect of autoregulation on intracellular LacI levels and also show that cAMP-CRP binding does not affect the efficiency of autoregulation. We built a mathematical model to study the role of LacI autoregulation in the lactose utilization system. Previously, it has been argued that negative autoregulation can significantly reduce noise as well as increase the speed of response. We show that the particular molecular mechanism, a transcriptional roadblock, used to achieve self-repression in the lac system does neither. Instead, LacI autoregulation balances two opposing states, one that allows quicker response to smaller pulses of external lactose, and the other that minimizes production costs in the absence of lactose.
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Affiliation(s)
- Szabolcs Semsey
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA, Department of Genetics, Eötvös Lóránd University, H-1117 Budapest, Hungary, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100 Gödöllő, Hungary and National Centre for Biological Sciences, Bangalore 560065, India
- *To whom correspondence should be addressed. Tel: +91 80 23666001/02; Fax: +91 80 23636662;
| | - Liselotte Jauffred
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA, Department of Genetics, Eötvös Lóránd University, H-1117 Budapest, Hungary, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100 Gödöllő, Hungary and National Centre for Biological Sciences, Bangalore 560065, India
| | - Zsolt Csiszovszki
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA, Department of Genetics, Eötvös Lóránd University, H-1117 Budapest, Hungary, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100 Gödöllő, Hungary and National Centre for Biological Sciences, Bangalore 560065, India
| | - János Erdőssy
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA, Department of Genetics, Eötvös Lóránd University, H-1117 Budapest, Hungary, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100 Gödöllő, Hungary and National Centre for Biological Sciences, Bangalore 560065, India
| | - Viktor Stéger
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA, Department of Genetics, Eötvös Lóránd University, H-1117 Budapest, Hungary, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100 Gödöllő, Hungary and National Centre for Biological Sciences, Bangalore 560065, India
| | - Sabine Hansen
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA, Department of Genetics, Eötvös Lóránd University, H-1117 Budapest, Hungary, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100 Gödöllő, Hungary and National Centre for Biological Sciences, Bangalore 560065, India
| | - Sandeep Krishna
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA, Department of Genetics, Eötvös Lóránd University, H-1117 Budapest, Hungary, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100 Gödöllő, Hungary and National Centre for Biological Sciences, Bangalore 560065, India
- Correspondence may also be addressed to Szabolcs Semsey. Tel: +45 24942613; Fax: +45 35325425;
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Csiszovszki Z, Lewis DEA, Le P, Sneppen K, Semsey S. Specific contacts of the -35 region of the galP1 promoter by RNA polymerase inhibit GalR-mediated DNA looping repression. Nucleic Acids Res 2012; 40:10064-72. [PMID: 22941635 PMCID: PMC3488240 DOI: 10.1093/nar/gks796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The P1 promoter of the galactose operon in Escherichia coli is one of the best studied examples of ‘extended −10’ promoters. Recognition of the P1 promoter does not require specific contacts between RNA polymerase and its poor −35 element. To investigate whether specific recognition of the −35 element would affect the regulation of P1 by GalR, we mutagenized the −35 element of P1, isolated variants of the −35 element and studied the regulation of the mutant promoters by in vitro transcription assays and by mathematical modeling. The results show that the GalR-mediated DNA loop is less efficient in repressing P1 transcription when RNA polymerase binds to the −10 and −35 elements concomitantly. Our results suggest that promoters that lack specific −35 element recognition allow decoupling of local chromosome structure from transcription initiation.
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Affiliation(s)
- Zsolt Csiszovszki
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
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Abstract
Some unidentified RNA molecules, together with the nucleoid protein HU, were suggested to be involved in the nucleoid structure of Escherichia coli. HU is a conserved protein known for its role in binding to DNA and maintaining negative supercoils in the latter. HU also binds to a few RNAs, but the full spectrum of its binding targets in the cell is not known. To understand any interaction of HU with RNA in the nucleoid structure, we immunoprecipitated potential HU-RNA complexes from cells and examined bound RNAs by hybridization to whole-genome tiling arrays. We identified associations between HU and 10 new intragenic and intergenic noncoding RNAs (ncRNAs), 2 of which are homologous to the annotated bacterial interspersed mosaic elements (BIMEs) and boxC DNA repeat elements. We confirmed direct binding of HU to BIME RNA in vitro. We also studied the nucleoid shape of HU and two of the ncRNA mutants (nc1 and nc5) by transmission electron microscopy and showed that both HU and the two ncRNAs play a role in nucleoid morphology. We propose that at least two of the ncRNA species complex with HU and help the formation or maintenance of the architecture of the E. coli chromosome. We also observed binding of HU with rRNA and tRNA segments, a few small RNAs, and a distinct small set of mRNAs, although the significance, if any, of these associations is not known.
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9
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A genetic network that balances two outcomes utilizes asymmetric recognition of operator sites. Biophys J 2012; 102:1580-9. [PMID: 22500758 DOI: 10.1016/j.bpj.2012.01.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 01/26/2012] [Accepted: 01/27/2012] [Indexed: 11/21/2022] Open
Abstract
Stability and induction of the lysogenic state of bacteriophage λ are balanced by a complex regulatory network. A key feature of this network is the mutually exclusive cooperative binding of a repressor dimer (CI) to one of two pairs of binding sites, O(R)1-O(R)2 or O(R)2-O(R)3. The structural features that underpin the mutually exclusive binding mode are not well understood. Recent studies have demonstrated that CI is an asymmetric dimer. The functional importance of the asymmetry is not fully clear. Due to the asymmetric nature of the CI dimer as well as its binding sites, there are two possible bound orientations. By fluorescence resonance energy transfer measurements we showed that CI prefers one bound orientation. We also demonstrated that the relative configuration of the binding sites is important for CI dimer-dimer interactions and consequent cooperative binding. We proposed that the operator configuration dictates the orientations of the bound CI molecules, which in turn dictates CI cooperative interaction between the O(R)1-O(R)2 or O(R)2-O(R)3, but not both. Modeling suggests that the relative orientation of the C- and N-terminal domains may play an important role in the mutually exclusive nature of the cooperative binding. This work correlates unique structural features of a transcription regulatory protein with the functional properties of a gene regulatory network.
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Multilevel autoregulation of λ repressor protein CI by DNA looping in vitro. Proc Natl Acad Sci U S A 2011; 108:14807-12. [PMID: 21873207 DOI: 10.1073/pnas.1111221108] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The prophage state of bacteriophage λ is extremely stable and is maintained by a highly regulated level of λ repressor protein, CI, which represses lytic functions. CI regulates its own synthesis in a lysogen by activating and repressing its promoter, P(RM). CI participates in long-range interactions involving two regions of widely separated operator sites by generating a loop in the intervening DNA. We investigated the roles of each individual site under conditions that permitted DNA loop formation by using in vitro transcription assays for the first time on supercoiled DNA that mimics in vivo situation. We confirmed that DNA loops generated by oligomerization of CI bound to its operators influence the autoactivation and autorepression of P(RM) regulation. We additionally report that different configurations of DNA loops are central to this regulation--one configuration further enhances autoactivation and another is essential for autorepression of P(RM).
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11
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Abstract
Gene regulatory networks are based on simple building blocks such as promoters, transcription factors (TFs) and their binding sites on DNA. But how diverse are the functions that can be obtained by different arrangements of promoters and TF binding sites? In this work we constructed synthetic regulatory regions using promoter elements and binding sites of two noninteracting TFs, each sensing a single environmental input signal. We show that simply by combining these three kinds of elements, we can obtain 11 of the 16 Boolean logic gates that integrate two environmental signals in vivo. Further, we demonstrate how combination of logic gates can result in new logic functions. Our results suggest that simple elements of transcription regulation form a highly flexible toolbox that can generate diverse functions under natural selection.
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Induction of the galactose enzymes in Escherichia coli is independent of the C-1-hydroxyl optical configuration of the inducer D-galactose. J Bacteriol 2008; 190:7932-8. [PMID: 18931131 DOI: 10.1128/jb.01008-08] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The two optical forms of aldohexose galactose differing at the C-1 position, alpha-D-galactose and beta-D-galactose, are widespread in nature. The two anomers also occur in di- and polysaccharides, as well as in glycoconjugates. The anomeric form of D-galactose, when present in complex carbohydrates, e.g., cell wall, glycoproteins, and glycolipids, is specific. Their interconversion occurs as monomers and is effected by the enzyme mutarotase (aldose-1-epimerase). Mutarotase and other D-galactose-metabolizing enzymes are coded by genes that constitute an operon in Escherichia coli. The operon is repressed by the repressor GalR and induced by D-galactose. Since, depending on the carbon source during growth, the cell can make only one of the two anomers of D-galactose, the cell must also convert one anomer to the other for use in specific biosynthetic pathways. Thus, it is imperative that induction of the gal operon, specifically the mutarotase, be achievable by either anomer of D-galactose. Here we report in vivo and in vitro experiments showing that both alpha-D-galactose and beta-D-galactose are capable of inducing transcription of the gal operon with equal efficiency and kinetics. Whereas all substitutions at the C-1 position in the alpha configuration inactivate the induction capacity of the sugar, the effect of substitutions in the beta configuration varies depending upon the nature of the substitution; methyl and phenyl derivatives induce weakly, but the glucosyl derivative does not.
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Lewis DEA, Komissarova N, Le P, Kashlev M, Adhya S. DNA sequences in gal operon override transcription elongation blocks. J Mol Biol 2008; 382:843-58. [PMID: 18691599 DOI: 10.1016/j.jmb.2008.07.060] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 06/12/2008] [Accepted: 07/23/2008] [Indexed: 12/01/2022]
Abstract
The DNA loop that represses transcription from galactose (gal) promoters is infrequently formed in stationary-phase cells because the concentration of the loop architectural protein HU is significantly low at that state, resulting in expression of the operon in the absence of the gal inducer D-galactose. Unexpectedly, transcription from the gal promoters under these conditions overrides physical block because of the presence of the Gal repressor bound to an internal operator (O(I)) located downstream of the promoters. We have shown here that although a stretch of pyrimidine residues (UUCU) in the RNA:DNA hybrid located immediately upstream of O(I) weakens the RNA:DNA hybrid and favors RNA polymerase (RNAP) pausing and backtracking, a stretch of purines (GAGAG) in the RNA present immediately upstream of the pause sequence in the hybrid acts as an antipause element by stabilizing the RNA:DNA duplex and preventing backtracking. This facilitates forward translocation of RNAP, including overriding of the DNA-bound Gal repressor barrier at O(I). When the GAGAG sequence is separated from the pyrimidine sequence by a 5-bp DNA insertion, RNAP backtracking is favored from a weak hybrid to a more stable hybrid. RNAP backtracking is sensitive to Gre factors, D-galactose, and antisense oligonucleotides. The ability of a native DNA sequence to override transcription elongation blocks in the gal operon uncovers a previously unknown way of regulating gal metabolism in Escherichia coli. It also explains the synthesis of gal enzymes in the absence of inducer for biosynthetic reactions.
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Affiliation(s)
- Dale E A Lewis
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA.
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14
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Abstract
The gal regulon of Escherichia coli contains genes involved in galactose transport and metabolism. Transcription of the gal regulon genes is regulated in different ways by two iso-regulatory proteins, Gal repressor (GalR) and Gal isorepressor (GalS), which recognize the same binding sites in the absence of d-galactose. DNA binding by both GalR and GalS is inhibited in the presence of d-galactose. Many of the gal regulon genes are activated in the presence of the adenosine cyclic-3',5'-monophosphate (cAMP)-cAMP receptor protein (CRP) complex. We studied transcriptional regulation of the gal regulon promoters simultaneously in a purified system and attempted to integrate the two small molecule signals, d-galactose and cAMP, that modulate the isoregulators and CRP respectively, at each promoter, using Boolean logic. Results show that similarly organized promoters can have different input functions. We also found that in some cases the activity of the promoter and the cognate gene can be described by different logic gates. We combined the transcriptional network of the galactose regulon, obtained from our experiments, with literature data to construct an integrated map of the galactose network. Structural analysis of the network shows that at the interface of the genetic and metabolic network, feedback loops are by far the most common motif.
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Affiliation(s)
- Szabolcs Semsey
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA
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Lee EH, Hill SA, Napier R, Shafer WM. Integration Host Factor is required for FarR repression of the farAB-encoded efflux pump of Neisseria gonorrhoeae. Mol Microbiol 2006; 60:1381-400. [PMID: 16796676 DOI: 10.1111/j.1365-2958.2006.05185.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The farAB operon encodes an efflux pump system that mediates the resistance of Neisseria gonorrhoeae to antimicrobial long-chain fatty acids. We previously observed that expression of farAB is negatively regulated by the FarR repressor. In this study, we examined the molecular mechanism by which FarR represses expression of farAB. DNase I footprinting analysis, coupled with a deletion analysis of the farAB promoter region, indicated that FarR binds to three sites (termed sites A, B and C) within the DNA sequence upstream of farA; genetic analysis revealed, however, that site B is not required for FarR repression of farAB. This repression also required the presence of Integration Host Factor (IHF), which was found to bind to sequences located between FarR binding sites A and C. We determined that IHF binding to the farAB promoter region could inhibit transcription in vitro and that such binding induced a bending of the target DNA, which we propose to be important in regulating this operon. IHF binding to the promoter region was found to stabilize the binding of FarR to its binding sites A and C and as a consequence, enhanced repression of farAB expression mediated by FarR. We propose a model in which expression of the farAB-encoded efflux pump in N. gonorrhoeae is modulated by the DNA binding activities of FarR and IHF.
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Affiliation(s)
- Eun-Hee Lee
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
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16
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Lewis DEA, Adhya S. Axiom of determining transcription start points by RNA polymerase in Escherichia coli. Mol Microbiol 2005; 54:692-701. [PMID: 15491360 DOI: 10.1111/j.1365-2958.2004.04318.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
To investigate the determining factors in the selection of the transcription start points (tsp) by RNA polymerase of Escherichia coli, we systematically deleted or substituted single base pairs (bps) at 25 putative critical positions in the two extended -10 promoters, P1 and P2, of the gal operon. These changes extend downstream from -24 to +1 of the P1 promoter. In vitro transcription assays using supercoiled DNA templates revealed a preference for a purine in the non-template strand for tsp in both promoters. The optimal tsp is the 11th bp counting downstream from the -10 position. A single bp deletion anywhere from -10 to +1 switched the tsp to the next available purine 2-3 bp downstream on the non-template strand whereas deleting a single bp at position from -24 to -11 did not affect the tsp. The nature of the 10 bp sequence of the -10 to -1 region, while affecting promoter strength, did not influence tsp. The cAMP-CRP complex, which stimulates P1 and represses P2, did not affect the tsp selection process. The rules of tsp selection by RNA polymerase containing sigma70 in gal and pyr promoters discussed here may be applicable to others.
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Affiliation(s)
- Dale E A Lewis
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA
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