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Schleif R. A Career's Work, the l-Arabinose Operon: How It Functions and How We Learned It. EcoSal Plus 2022; 10:eESP00122021. [PMID: 36519894 PMCID: PMC10729937 DOI: 10.1128/ecosalplus.esp-0012-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/20/2021] [Indexed: 06/17/2023]
Abstract
Very few labs have had the good fortune to have been able to focus for more than 50 years on a relatively narrow research topic and to be in a field in which both basic knowledge and the research technology and methods have progressed as rapidly as they have in molecular biology. My research group, first at Brandeis University and then at Johns Hopkins University, has had this opportunity. In this review, therefore, I will describe largely the work from my laboratory that has spanned this period and which was carried out by 40 plus graduate students, several postdoctoral associates, my technician, and me. In addition to presenting the scientific findings or results, I will place many of the topics in scientific context and, because we needed to develop a good many of the experimental methods behind our findings, I will also describe some of these methods and their importance. Also included will be occasional comments on how the research community or my research group functioned. Because a wide variety of approaches were used throughout our work, no ideal organization of this review is apparent. Therefore, I have chosen to use a hybrid structure in which there are six sections. Within each of the sections, experiments and findings will be described roughly in chronological order. Frequent cross references between parts and sections will be made because some findings and experimental approaches could logically have been described in more than one place.
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Shimizu K. Metabolic Regulation and Coordination of the Metabolism in Bacteria in Response to a Variety of Growth Conditions. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 155:1-54. [PMID: 25712586 DOI: 10.1007/10_2015_320] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Living organisms have sophisticated but well-organized regulation system. It is important to understand the metabolic regulation mechanisms in relation to growth environment for the efficient design of cell factories for biofuels and biochemicals production. Here, an overview is given for carbon catabolite regulation, nitrogen regulation, ion, sulfur, and phosphate regulations, stringent response under nutrient starvation as well as oxidative stress regulation, redox state regulation, acid-shock, heat- and cold-shock regulations, solvent stress regulation, osmoregulation, and biofilm formation, and quorum sensing focusing on Escherichia coli metabolism and others. The coordinated regulation mechanisms are of particular interest in getting insight into the principle which governs the cell metabolism. The metabolism is controlled by both enzyme-level regulation and transcriptional regulation via transcription factors such as cAMP-Crp, Cra, Csr, Fis, P(II)(GlnB), NtrBC, CysB, PhoR/B, SoxR/S, Fur, MarR, ArcA/B, Fnr, NarX/L, RpoS, and (p)ppGpp for stringent response, where the timescales for enzyme-level and gene-level regulations are different. Moreover, multiple regulations are coordinated by the intracellular metabolites, where fructose 1,6-bisphosphate (FBP), phosphoenolpyruvate (PEP), and acetyl-CoA (AcCoA) play important roles for enzyme-level regulation as well as transcriptional control, while α-ketoacids such as α-ketoglutaric acid (αKG), pyruvate (PYR), and oxaloacetate (OAA) play important roles for the coordinated regulation between carbon source uptake rate and other nutrient uptake rate such as nitrogen or sulfur uptake rate by modulation of cAMP via Cya.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan. .,Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan.
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The transport and mediation mechanisms of the common sugars in Escherichia coli. Biotechnol Adv 2014; 32:905-19. [DOI: 10.1016/j.biotechadv.2014.04.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 03/23/2014] [Accepted: 04/18/2014] [Indexed: 11/17/2022]
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Fritz G, Megerle JA, Westermayer SA, Brick D, Heermann R, Jung K, Rädler JO, Gerland U. Single cell kinetics of phenotypic switching in the arabinose utilization system of E. coli. PLoS One 2014; 9:e89532. [PMID: 24586851 PMCID: PMC3935871 DOI: 10.1371/journal.pone.0089532] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/22/2014] [Indexed: 12/05/2022] Open
Abstract
Inducible switching between phenotypes is a common strategy of bacteria to adapt to fluctuating environments. Here, we analyze the switching kinetics of a paradigmatic inducible system, the arabinose utilization system in E. coli. Using time-lapse fluorescence microscopy of microcolonies in a microfluidic chamber, which permits sudden up- and down-shifts in the inducer arabinose, we characterize the single-cell gene expression dynamics of the araBAD operon responsible for arabinose degradation. While there is significant, inducer-dependent cell-to-cell variation in the timing of the on-switching, the off-switching triggered by sudden removal of arabinose is homogeneous and rapid. We find that rapid off-switching does not depend on internal arabinose degradation. Because the system is regulated via the internal arabinose level sensed by AraC, internal arabinose must be rapidly depleted by leakage or export from the cell, or by degradation via a non-canonical pathway. We explored whether the poorly characterized membrane protein AraJ, which is part of the arabinose regulon and has been annotated as a possible arabinose efflux protein, is responsible for rapid depletion. However, we find that AraJ is not essential for rapid switching to the off-state. We develop a mathematical model for the arabinose system, which quantitatively describes both the heterogeneous on-switching and the homogeneous off-switching. The model also predicts that mutations which disrupt the positive feedback of internal arabinose on the production of arabinose uptake proteins change the heterogeneous on-switching behavior into a homogeneous, graded response. We construct such a mutant and confirm the graded response experimentally. Taken together, our results indicate that the physiological switching behavior of this sugar utilization system is asymmetric, such that off-switching is always rapid and homogeneous, while on-switching is slow and heterogeneously timed at sub-saturating inducer levels.
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Affiliation(s)
- Georg Fritz
- Arnold Sommerfeld Center for Theoretical Physics and CeNS, Ludwig- Maximilians-Universität München, Munich, Germany
- Center for Integrated Protein Science (CiPSM) at the Department of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Judith A. Megerle
- Faculty of Physics and CeNS, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sonja A. Westermayer
- Faculty of Physics and CeNS, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Delia Brick
- Faculty of Physics and CeNS, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ralf Heermann
- Center for Integrated Protein Science (CiPSM) at the Department of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Kirsten Jung
- Center for Integrated Protein Science (CiPSM) at the Department of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Joachim O. Rädler
- Faculty of Physics and CeNS, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ulrich Gerland
- Arnold Sommerfeld Center for Theoretical Physics and CeNS, Ludwig- Maximilians-Universität München, Munich, Germany
- * E-mail:
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Mäkelä J, Kandhavelu M, Oliveira SMD, Chandraseelan JG, Lloyd-Price J, Peltonen J, Yli-Harja O, Ribeiro AS. In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter. Nucleic Acids Res 2013; 41:6544-52. [PMID: 23644285 PMCID: PMC3711423 DOI: 10.1093/nar/gkt350] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Using a single-RNA detection technique in live Escherichia coli cells, we measure, for each cell, the waiting time for the production of the first RNA under the control of PBAD promoter after induction by arabinose, and subsequent intervals between transcription events. We find that the kinetics of the arabinose intake system affect mean and diversity in RNA numbers, long after induction. We observed the same effect on Plac/ara-1 promoter, which is inducible by arabinose or by IPTG. Importantly, the distribution of waiting times of Plac/ara-1 is indistinguishable from that of PBAD, if and only if induced by arabinose alone. Finally, RNA production under the control of PBAD is found to be a sub-Poissonian process. We conclude that inducer-dependent waiting times affect mean and cell-to-cell diversity in RNA numbers long after induction, suggesting that intake mechanisms have non-negligible effects on the phenotypic diversity of cell populations in natural, fluctuating environments.
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Affiliation(s)
- Jarno Mäkelä
- Laboratory of Biosystem Dynamics, Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, FI-33101 Tampere, Finland
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Damjanovic A, Miller BT, Schleif R. Understanding the basis of a class of paradoxical mutations in AraC through simulations. Proteins 2013; 81:490-8. [PMID: 23150197 PMCID: PMC3557760 DOI: 10.1002/prot.24207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 09/15/2012] [Accepted: 10/02/2012] [Indexed: 11/10/2022]
Abstract
Most mutations at position 15 in the N-terminal arm of the regulatory protein AraC leave the protein incapable of responding to arabinose and inducing the proteins required for arabinose catabolism. Mutations at other positions of the arm do not have this behavior. Simple energetic analysis of the interactions between the arm and bound arabinose do not explain the uninducibility of AraC with mutations at position 15. Extensive molecular dynamics (MD) simulations, carried out largely on the Open Science Grid, were done of the wild-type protein with and without bound arabinose and of all possible mutations at position 15, many of which were constructed and measured for this work. Good correlation was found for deviation of arm position during the simulations and inducibility as measured in vivo of the same mutant proteins. Analysis of the MD trajectories revealed that preservation of the shape of the arm is critical to inducibility. To maintain the correct shape of the arm, the strengths of three interactions observed to be strong in simulations of the wild-type AraC protein need to be preserved. These interactions are between arabinose and residue 15, arabinose and residues 8-9, and residue 13 and residue 15. The latter interaction is notable because residues L9, Y13, F15, W95, and Y97 form a hydrophobic cluster which needs to be preserved for retention of the correct shape.
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Affiliation(s)
- Ana Damjanovic
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Benjamin T. Miller
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Robert Schleif
- Biology Department, Johns Hopkins University, Baltimore, Maryland
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Yildirim N. Mathematical modeling of the low and high affinity arabinose transport systems in Escherichia coli. MOLECULAR BIOSYSTEMS 2012; 8:1319-24. [PMID: 22314998 DOI: 10.1039/c2mb05352g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mathematical model was developed for the low and high affinity arabinose transport systems in E. coli. The model is a system of three ordinary differential equations and takes the dynamics of mRNAs for the araE and araFGH proteins and the internal arabinose into account. Special attention was paid to estimate the model parameters from the literature. Our analysis and simulations suggest that the high affinity transport system helps the low affinity transport system to respond to high concentration of extracellular arabinose faster, whereas the high affinity transport system responds to a small amount of extracellular arabinose. Steady state analysis of the model also predicts that there is a regime for the extracellular concentration of arabinose where the arabinose system can show bistable behavior.
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Affiliation(s)
- Necmettin Yildirim
- Division of Natural Sciences, New College of Florida, Sarasota, FL 34243, USA.
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Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli. BMC SYSTEMS BIOLOGY 2011; 5:111. [PMID: 21749723 PMCID: PMC3163201 DOI: 10.1186/1752-0509-5-111] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 07/12/2011] [Indexed: 11/27/2022]
Abstract
Background Gene regulation networks are made of recurring regulatory patterns, called network motifs. One of the most common network motifs is negative auto-regulation, in which a transcription factor represses its own production. Negative auto-regulation has several potential functions: it can shorten the response time (time to reach halfway to steady-state), stabilize expression against noise, and linearize the gene's input-output response curve. This latter function of negative auto-regulation, which increases the range of input signals over which downstream genes respond, has been studied by theory and synthetic gene circuits. Here we ask whether negative auto-regulation preserves this function also in the context of a natural system, where it is embedded within many additional interactions. To address this, we studied the negative auto-regulation motif in the arabinose utilization system of Escherichia coli, in which negative auto-regulation is part of a complex regulatory network. Results We find that when negative auto-regulation is disrupted by placing the regulator araC under constitutive expression, the input dynamic range of the arabinose system is reduced by 10-fold. The apparent Hill coefficient of the induction curve changes from about n = 1 with negative auto-regulation, to about n = 2 when it is disrupted. We present a mathematical model that describes how negative auto-regulation can increase input dynamic-range, by coupling the transcription factor protein level to the input signal. Conclusions Here we demonstrate that the negative auto-regulation motif in the native arabinose system of Escherichia coli increases the range of arabinose signals over which the system can respond. In this way, negative auto-regulation may help to increase the input dynamic-range while maintaining the specificity of cooperative regulatory systems. This function may contribute to explaining the common occurrence of negative auto-regulation in biological systems.
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Schleif R. AraC protein, regulation of the l-arabinose operon in Escherichia coli, and the light switch mechanism of AraC action. FEMS Microbiol Rev 2010; 34:779-96. [PMID: 20491933 DOI: 10.1111/j.1574-6976.2010.00226.x] [Citation(s) in RCA: 187] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
This review covers the physiological aspects of regulation of the arabinose operon in Escherichia coli and the physical and regulatory properties of the operon's controlling gene, araC. It also describes the light switch mechanism as an explanation for many of the protein's properties. Although many thousands of homologs of AraC exist and regulate many diverse operons in response to many different inducers or physiological states, homologs that regulate arabinose-catabolizing genes in response to arabinose were identified. The sequence similarities among them are discussed in light of the known structure of the dimerization and DNA-binding domains of AraC.
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Affiliation(s)
- Robert Schleif
- Biology Department, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
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10
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Abstract
In the bacterium Escherichia coli, the AraC protein positively and negatively regulates expression of the proteins required for the uptake and catabolism of the sugar L-arabinose. This essay describes how work from my laboratory on this system spanning more than thirty years has aided our understanding of positive regulation, revealed DNA looping (a mechanism that explains many action-at-a-distance phenomena) and, more recently, has uncovered the mechanism by which arabinose shifts AraC from a state where it prefers to bind to two well-separated DNA half-sites and form a DNA loop to a state where it binds to two adjacent half-sites and activates transcription. This work required learning how to assay, purify, and work with a protein possessing highly uncooperative biochemical properties. Present work is focussed on understanding arabinose-responsive mechanism in atomic detail and is also directed towards understanding protein structure and function well enough to be able to engineer the allosteric mechanism seen in AraC onto other proteins.
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Affiliation(s)
- Robert Schleif
- Biology Department, Johns Hopkins University, 3400 N. Charles St. Baltimore, MD 21218, USA
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Vermersch PS, Lemon DD, Tesmer JJG, Quiocho FA. Sugar-binding and crystallographic studies of an arabinose-binding protein mutant (Met108Leu) that exhibits enhanced affinity and altered specificity. Biochemistry 2002. [DOI: 10.1021/bi00242a009] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bayele HK. Critical parameters for functional reconstitution of glucose transport in Trypanosoma brucei membrane vesicles. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1513:223-31. [PMID: 11470094 DOI: 10.1016/s0005-2736(01)00363-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The glucose transporter of Trypanosoma brucei was reconstituted by incorporating Escherichia coli phospholipid liposomes into detergent-solubilised trypanosome membranes. Proteoliposome vesicles were formed by detergent dilution and used in glucose-uptake assays. The minima for functional reconstitution of the glucose transporter were established and used to probe the mechanism of glucose transport. The uptake pattern of radiolabelled glucose showed a counterflow transient at about 3 s, after which the sugar equilibrated across the proteoliposomal membrane. This observation is consistent with a facilitated transporter. There was a six-fold increase in the initial rate of glucose uptake compared to non-reconstituted or native membranes. In addition, the transporter exhibited stereospecificity to D-glucose but poorly transported L-glucose. Directionality, stereoselectivity or substrate specificity and cis-inhibition by phloridzin were therefore the main criteria for validation of glucose transport. The observed counterflow transient also provided further evidence for a facilitated glucose transporter within the trypanosome plasma membrane, and was the single most important criterion for this assertion. A stoichiometry of 0.78 mol of glucose per mol of transporter was estimated.
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Affiliation(s)
- H K Bayele
- Department of Biochemistry, University of Bath, Bath, UK.
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Khlebnikov A, Risa O, Skaug T, Carrier TA, Keasling JD. Regulatable arabinose-inducible gene expression system with consistent control in all cells of a culture. J Bacteriol 2000; 182:7029-34. [PMID: 11092865 PMCID: PMC94830 DOI: 10.1128/jb.182.24.7029-7034.2000] [Citation(s) in RCA: 127] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The arabinose-inducible promoter P(BAD) is subject to all-or-none induction, in which intermediate concentrations of arabinose give rise to subpopulations of cells that are fully induced and uninduced. To construct a host-vector expression system with regulatable control in a homogeneous population of cells, the araE gene of Escherichia coli was cloned into an RSF1010-derived plasmid under control of the isopropyl-beta-D-thiogalactopyranoside-inducible P(tac) and P(taclac) promoters. This gene encodes the low-affinity, high-capacity arabinose transport protein and is controlled natively by an arabinose-inducible promoter. To detect the effect of arabinose-independent araE expression on population homogeneity and cell-specific expression, the gfpuv gene was placed under control of the arabinose-inducible araBAD promoter (P(BAD)) on the pMB1-derived plasmid pBAD24. The transporter and reporter plasmids were transformed into E. coli strains with native arabinose transport systems and strains deficient in one or both of the arabinose transport systems (araE and/or araFGH). The effects of the arabinose concentration and arabinose-independent transport control on population homogeneity were investigated in these strains using flow cytometry. The araE, and araE araFGH mutant strains harboring the transporter and reporter plasmids were uniformly induced across the population at all inducer concentrations, and the level of gene expression in individual cells varied with arabinose concentration. In contrast, the parent strain, which expressed the native araE and araFGH genes and harbored the transporter and reporter plasmids, exhibited all-or-none behavior. This work demonstrates the importance of including a transport gene that is controlled independently of the inducer to achieve regulatable and consistent induction in all cells of the culture.
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Affiliation(s)
- A Khlebnikov
- Department of Chemical Engineering, University of California, Berkeley, California 94720-1462, USA
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Gallegos MT, Schleif R, Bairoch A, Hofmann K, Ramos JL. Arac/XylS family of transcriptional regulators. Microbiol Mol Biol Rev 1997; 61:393-410. [PMID: 9409145 PMCID: PMC232617 DOI: 10.1128/mmbr.61.4.393-410.1997] [Citation(s) in RCA: 362] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The ArC/XylS family of prokaryotic positive transcriptional regulators includes more than 100 proteins and polypeptides derived from open reading frames translated from DNA sequences. Members of this family are widely distributed and have been found in the gamma subgroup of the proteobacteria, low- and high-G + C-content gram-positive bacteria, and cyanobacteria. These proteins are defined by a profile that can be accessed from PROSITE PS01124. Members of the family are about 300 amino acids long and have three main regulatory functions in common: carbon metabolism, stress response, and pathogenesis. Multiple alignments of the proteins of the family define a conserved stretch of 99 amino acids usually located at the C-terminal region of the regulator and connected to a nonconserved region via a linker. The conserved stretch contains all the elements required to bind DNA target sequences and to activate transcription from cognate promoters. Secondary analysis of the conserved region suggests that it contains two potential alpha-helix-turn-alpha-helix DNA binding motifs. The first, and better-fitting motif is supported by biochemical data, whereas existing biochemical data neither support nor refute the proposal that the second region possesses this structure. The phylogenetic relationship suggests that members of the family have recruited the nonconserved domain(s) into a series of existing domains involved in DNA recognition and transcription stimulation and that this recruited domain governs the role that the regulator carries out. For some regulators, it has been demonstrated that the nonconserved region contains the dimerization domain. For the regulators involved in carbon metabolism, the effector binding determinants are also in this region. Most regulators belonging to the AraC/XylS family recognize multiple binding sites in the regulated promoters. One of the motifs usually overlaps or is adjacent to the -35 region of the cognate promoters. Footprinting assays have suggested that these regulators protect a stretch of up to 20 bp in the target promoters, and multiple alignments of binding sites for a number of regulators have shown that the proteins recognize short motifs within the protected region.
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Affiliation(s)
- M T Gallegos
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaìdín, Granada, Spain
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Muiry JA, Gunn TC, McDonald TP, Bradley SA, Tate CG, Henderson PJ. Proton-linked L-rhamnose transport, and its comparison with L-fucose transport in Enterobacteriaceae. Biochem J 1993; 290 ( Pt 3):833-42. [PMID: 8384447 PMCID: PMC1132357 DOI: 10.1042/bj2900833] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
1. An alkaline pH change occurred when L-rhamnose, L-mannose or L-lyxose was added to L-rhamnose-grown energy-depleted suspensions of strains of Escherichia coli. This is diagnostic of sugar-H+ symport activity. 2. L-Rhamnose, L-mannose and L-lyxose were inducers of the sugar-H+ symport and of L-[14C]rhamnose transport activity. L-Rhamnose also induced the biochemically and genetically distinct L-fucose-H+ symport activity in strains competent for L-rhamnose metabolism. 3. Steady-state kinetic measurements showed that L-mannose and L-lyxose were competitive inhibitors (alternative substrates) for the L-rhamnose transport system, and that L-galactose and D-arabinose were competitive inhibitors (alternative substrates) for the L-fucose transport system. Additional measurements with other sugars of related structure defined the different substrate specificities of the two transport systems. 4. The relative rates of H+ symport and of sugar metabolism, and the relative values of their kinetic parameters, suggested that the physiological role of the transport activity was primarily for utilization of L-rhamnose, not for L-mannose or L-lyxose. 5. L-Rhamnose transport into subcellular vesicles of E. coli was dependent on respiration, was optimal at pH 7, and was inhibited by protonophores and ionophores. It was insensitive to N-ethylmaleimide or cytochalasin B. 6. L-Rhamnose, L-mannose and L-lyxose each elicited an alkaline pH change when added to energy-depleted suspensions of L-rhamnose-grown Salmonella typhimurium LT2, Klebsiella pneumoniae, Klebsiella aerogenes, Erwinia carotovora carotovora and Erwinia carotovora atroseptica. The relative rates of subsequent acidification varied, depending on both the organism and the sugar. L-Fucose promoted an alkaline pH change in all the L-rhamnose-induced organisms except the Erwinia species. No L-rhamnose-H+ symport occurred in any organism grown on L-fucose. 7. All these results showed that L-rhamnose transport into the micro-organisms occurred by a system different from that for L-fucose transport. Both systems are energized by the trans-membrane electrochemical gradient of protons. 8. Neither steady-state kinetic measurements nor binding-protein assays revealed the existence of a second L-rhamnose transport system in E. coli.
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Affiliation(s)
- J A Muiry
- Department of Biochemistry, University of Cambridge, U.K
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Abstract
The Escherichia coli araFGH operon codes for proteins involved in the L-arabinose high-affinity transport system. Transcriptional regulation of the operon was studied by creating point mutations and deletions in the control region cloned into a GalK expression vector. The transcription start site was confirmed by RNA sequencing of transcripts. The sequences essential for polymerase function were localized by deletions and point mutations. Surprisingly, only a weak -10 consensus sequence, and no -35 sequence is required. Mutation of a guanosine at position -12 greatly reduced promoter activity, which suggests important polymerase interactions with DNA between the usual -10 and -35 positions. A double mutation toward the consensus in the -10 region was required to create a promoter capable of significant AraC-independent transcription. These results show that the araFGH promoter structure is similar to that of the galP1 promoter and is substantially different from that of the araBAD promoter. The effects of 11 mutations within the DNA region thought to bind the cyclic AMP receptor protein correlate well with the CRP consensus binding sequence and confirm that this region is responsible for cyclic AMP regulation. Deletion of the AraC binding site nearest the promoter, araFG1, eliminates arabinose regulation, whereas deletion of the upstream AraC binding site, araFG2, has only a slight effect on promoter activity.
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Affiliation(s)
- W Hendrickson
- Department of Microbiology and Immunology, College of Medicine, University of Illinois, Chicago 60680
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Reeder T, Schleif R. Mapping, sequence, and apparent lack of function of araJ, a gene of the Escherichia coli arabinose regulon. J Bacteriol 1991; 173:7765-71. [PMID: 1744033 PMCID: PMC212566 DOI: 10.1128/jb.173.24.7765-7771.1991] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We report the mapping, sequencing, and study of the physiological role of the fourth arabinose-inducible operon from Escherichia coli, araJ. It is located at 9 min on the chromosome and codes for a single 42-kDa protein that shows no significant homology to other known proteins. Destruction of the chromosomal araJ gene does not detectably affect either of the two arabinose transport systems, the ability of cells to grow on arabinose, or the induction kinetics of the araBAD operon, and thus the physiological role of AraJ, if any, remains unknown. We have also found a long open reading frame upstream of araJ. The sequence of this upstream open reading frame was found to be identical to the previously reported sequence of the sbcC gene (I. S. Naom, S. J. Morton, D. R. F. Leach, and R. G. Lloyd, Nucleic Acids Res. 17:8033-8044, 1989). The carboxyl region of SbcC has an amino acid sequence consistent with this region of SbcC forming an extended alpha-helical coiled-coil.
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Affiliation(s)
- T Reeder
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218
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Vermersch PS, Tesmer JJ, Lemon DD, Quiocho FA. A Pro to Gly mutation in the hinge of the arabinose-binding protein enhances binding and alters specificity. Sugar-binding and crystallographic studies. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)46264-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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19
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Abstract
Expression plasmids containing various portions of araFGH operon sequences were assayed for their ability to facilitate the high-affinity L-arabinose transport process in a strain lacking the chromosomal copy of this operon. Accumulation studies demonstrated that the specific induction of all three operon coding sequences was necessary to restore high-affinity L-arabinose transport. Kinetic analysis of this genetically reconstituted transport system indicated that it functions with essentially wild-type parameters. Therefore, L-arabinose-binding protein-mediated transport appears to require only two inducible membrane-associated components (araG and araH) in addition to the binding protein (araF).
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Affiliation(s)
- B F Horazdovsky
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106
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20
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Maiden MC, Jones-Mortimer MC, Henderson PJ. The cloning, DNA sequence, and overexpression of the gene araE coding for arabinose-proton symport in Escherichia coli K12. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68433-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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21
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Bradley SA, Tinsley CR, Muiry JA, Henderson PJ. Proton-linked L-fucose transport in Escherichia coli. Biochem J 1987; 248:495-500. [PMID: 2829831 PMCID: PMC1148569 DOI: 10.1042/bj2480495] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
1. Addition of L-fucose to energy-depleted anaerobic suspensions of Escherichia coli elicited an uncoupler-sensitive alkaline pH change diagnostic of L-fucose/H+ symport activity. 2. L-Galactose or D-arabinose were also substrates, but not inducers, for the L-fucose/H+ symporter. 3. L-Fucose transport into subcellular vesicles was dependent upon respiration, displayed a pH optimum of about 5.5, and was inhibited by protonophores and ionophores. 4. These results showed that L-fucose transport into E. coli was energized by the transmembrane electrochemical gradient of protons. 5. Neither steady state kinetic measurements nor assays of L-fucose binding to periplasmic proteins revealed the existence of a second L-fucose transport system.
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Affiliation(s)
- S A Bradley
- Department of Biochemistry, University of Cambridge, U.K
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22
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Scripture JB, Voelker C, Miller S, O'Donnell RT, Polgar L, Rade J, Horazdovsky BF, Hogg RW. High-affinity L-arabinose transport operon. Nucleotide sequence and analysis of gene products. J Mol Biol 1987; 197:37-46. [PMID: 2445996 DOI: 10.1016/0022-2836(87)90607-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The nucleotide sequence of the "high-affinity" L-arabinose transport operon has been determined 3' from the regulatory region and found to contain three open reading frames designated araF, araG and araH. The first gene 3' to the regulatory region, araF, encodes the 23-residue signal peptide and the 306-residue mature form of the L-arabinose binding protein (33,200 Mr). The binding protein, which has been described elsewhere, is hydrophilic, soluble and found in the periplasm of Escherichia coli. This gene is followed by an intragenic space of 72 nucleotides, which contains a region of dyad symmetry 23 nucleotides long capable of forming an 11-member stem-loop. The second gene, designated araG, contains an open reading frame capable of encoding an equally hydrophilic protein containing 504 residues (55,000 Mr). Following a 14-nucleotide spacer, which does not appear to have any secondary structure, the third open reading frame, herein designated araH, is capable of encoding a hydrophobic protein containing 329 residues (34,000 Mr) that can only be envisioned as having an integral membrane location. 3' to araH there is a T-rich region containing a 24-nucleotide area of dyad symmetry centered 55 nucleotides from the termination codon. Analysis of the derived primary sequences of the araG and araH products indicates the nature and potential features of these components. The araG protein was found to possess internal homology between its amino and carboxyl-terminal halves, suggesting a common origin. The araG gene product has been shown to be homologous to the rbsA gene product, the hisP product, the ptsB product and the malK product, all of which presumably play similar roles in their respective transport systems. Putative ATP binding sites are observed within the regions of homology. The araH gene product has been shown to be homologous to the rbsC gene product, which is the first observed homology between two purported membrane proteins.
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Affiliation(s)
- J B Scripture
- Department of Molecular Biology and Microbiology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106
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23
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Abstract
Various portions of the "high-affinity" L-arabinose transport operon were cloned into the plasmid expression vector pKK223-3 and the operon-encoded protein products were identified. The results indicate that three proteins are encoded by this operon. The first is a 33,000 Mr protein that is the product of the promoter-proximal L-arabinose binding protein coding sequence, araF. A 52,000 Mr protein is encoded by sequence 3' to araF and has been assigned to the araG locus. The sequence 3' to araG encodes a 31,000 Mr protein that has been assigned to the araH locus. Both the araG and araH gene products are localized in the membrane fraction of the cell, implying a role in the membrane-associated complex of the high-affinity L-arabinose transport system. Nuclease S1 protection studies indicate that two operon message populations are present in the cell, a full-length operon transcript and a seven- to tenfold more abundant binding protein-specific message. The relative abundance of these two message populations correlates with the differential expression of the binding protein and the membrane-associated proteins of the transport system.
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Affiliation(s)
- B F Horazdovsky
- Department of Molecular Biology and Microbiology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106
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24
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Henderson PJ, Macpherson AJ. Assay, genetics, proteins, and reconstitution of proton-linked galactose, arabinose, and xylose transport systems of Escherichia coli. Methods Enzymol 1986; 125:387-429. [PMID: 3520228 DOI: 10.1016/s0076-6879(86)25033-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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25
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Davis EO, Jones-Mortimer MC, Henderson PJ. Location of a structural gene for xylose-H+ symport at 91 min on the linkage map of Escherichia coli K12. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)43439-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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26
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Stoner CM, Schleif RF. Transcription start site and induction kinetics of the araC regulatory gene in Escherichia coli K-12. J Mol Biol 1983; 170:1049-53. [PMID: 6196488 DOI: 10.1016/s0022-2836(83)80205-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The in vivo transcription start site of the araC message was determined by S1 nuclease mapping of hybrids formed between labeled DNA, and RNA extracted from cells grown under a variety of physiological conditions, including the interval of transient derepression following arabinose addition. Under all conditions tested, transcription initiated from the same nucleotide position at -148.
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27
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Fukada H, Sturtevant JM, Quiocho FA. Thermodynamics of the binding of L-arabinose and of D-galactose to the L-arabinose-binding protein of Escherichia coli. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44100-7] [Citation(s) in RCA: 95] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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28
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Schecter JB. Suppressed nonsense mutations in the araC gene of Escherichia coli provide three novel variant proteins. J Bacteriol 1983; 154:1329-38. [PMID: 6343350 PMCID: PMC217608 DOI: 10.1128/jb.154.3.1329-1338.1983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A total of 400 suppressible mutations have been isolated in the araC gene of Escherichia coli. Based on deletion mapping, growth patterns when suppressed, and intragenic recombination, 37 mutants have been determined to contain unique mutations. Rapid plate assays were developed to test for each of the three AraC protein functions: inducing araBAD, repressing araBAD, and araC self-repression. The 185 mutant proteins, resulting from 37 mutants each suppressed by five different suppressors, were assayed for each of the three AraC functions. These plate assays showed that: (i) for each function, some areas of the gene map are more sensitive to mutation than other areas, and (ii) three of the mutant AraC proteins were unlike previously characterized AraC mutants. Enzyme assays on the mutant proteins confirmed their novel character. The first mutant cannot induce araBAD but retains the capacity to perform both repression functions; and the second and third can each perform one of the two repression functions better than it can perform the other. These characteristics suggest that previously proposed models of ara regulation are incomplete.
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29
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Kosiba BE, Schleif R. Arabinose-inducible promoter from Escherichia coli. Its cloning from chromosomal DNA, identification as the araFG promoter and sequence. J Mol Biol 1982; 156:53-66. [PMID: 7047752 DOI: 10.1016/0022-2836(82)90458-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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30
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Ahlem C, Huisman W, Neslund G, Dahms AS. Purification and properties of a periplasmic D-xylose-binding protein from Escherichia coli K-12. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(19)81053-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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31
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Lee JH, Russo RJ, Heffernan L, Wilcox G. Regulation of L-arabinose transport in Salmonella typhimurium LT2. MOLECULAR & GENERAL GENETICS : MGG 1982; 185:136-41. [PMID: 6283309 DOI: 10.1007/bf00333803] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The inducible L-arabinose transport system was characterized in Salmonella typhimurium LT2. Only one L-arabinose transport system with a Km of 2 X 10(-4) M was identified. The results suggested that araE may be the only gene which codes for L-arabinose transport activity under the conditions tested. An araE-lac fusion strain was used to study the induction of the araE gene. No araE expression was detected when the L-arabinose concentration was lower than 1 mM. The expression of araE reached a maximum in the presence of 50 mM L-arabinose, and was significantly reduced in the presence of 50 mM L-arabinose, and was significantly reduced in the presence of D-glucose. Expression of the araBAD and araE genes was coordinately regulated. The concentration of L-arabinose that allowed maximum araBAD gene expression was 50-fold lower in an araE+ strain compared to an araE strain.
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32
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33
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Daruwalla KR, Paxton AT, Henderson PJ. Energization of the transport systems for arabinose and comparison with galactose transport in Escherichia coli. Biochem J 1981; 200:611-27. [PMID: 6282256 PMCID: PMC1163584 DOI: 10.1042/bj2000611] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
1. Strains of Escherichia coli were obtained containing either the AraE or the AraF transport system for arabinose. AraE+,AraF- strains effected energized accumulation and displayed an arabinose-evoked alkaline pH change indicative of arabinose-H+ symport. In contrast, AraE-,AraF+ strains accumulated arabinose but did not display H+ symport. 2. The ability of different sugars and their derivatives to elicit sugar-H+ symport in AraE+ strains was examined. Only L-arabinose and D-fucose were good substrates, and arabinose was the only inducer. 3. Membrane vesicles prepared from an AraE+,AraF+ strain accumulated the sugar, energized most efficiently by the respiratory substrates ascorbate + phenazine methosulphate. Addition of arabinose or fucose to an anaerobic suspension of membrane vesicles caused an alkaline pH change indicative or sugar-H+ symport on the membrane-bound transport system. 4. Kinetic studies and the effects of arsenate and uncoupling agents in intact cells and membrane vesicles gave further evidence that AraE is a low-affinity membrane-bound sugar-H+ symport system and that AraF is a binding-protein-dependent high-affinity system that does not require a transmembrane protonmotive force for energization. 5. The interpretation of these results is that arabinose transport into E. coli is energized by an electrochemical gradient of protons (AraE system) or by phosphate bond energy (AraF system). 6. In batch cultures the rates of growth and carbon cell yields on arabinose were lower in AraE-,AraF+ strains than in AraE+,AraF- or AraE+,AraF+ strains. The AraF system was more susceptible to catabolite repression than was the AraE system. 7. The properties of the two transport systems for arabinose are compared with those of the genetically and biochemically distinct transport systems for galactose, GalP and MglP. It appears that AraE is analogous to GalP, and AraF to MglP.
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34
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Gausing K. Construction and characterization of a tufA-lacZ fusion coding for an E. coli EF-Tu-beta-galactosidase chimeric protein. MOLECULAR & GENERAL GENETICS : MGG 1981; 184:265-71. [PMID: 6276696 DOI: 10.1007/bf00272915] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A new phage lambda cloning vector was constructed that has a single EcoRI site upstream from weakly expressed lacI-Z gene isolated by Müller-Hill and Kania (1974). An EcoRI fragment containing the complete tufA gene of E. coli was cloned on the vector and the recombinant phage was crossed into the str operon that has tufA as its last gene. Subsequent selection gave rise to a tufA-lacZ fusion that codes for a chimeric peptide. The fused peptide has a molecular weight of 148,000 and contains 40% of the N-terminal of EF-Tu followed by part of the lac repressor-beta-galactosidase fusion. The specific activity of the fused peptide is about half of the activity of normal beta-galactosidase.
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35
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Abstract
Mutations in the arabinose transport operons of Escherichia coli K-12 were isolated with the Mu lac phage by screening for cells in which beta-galactosidase is induced in the presence of L-arabinose. Standard genetic techniques were then used to isolate numerous mutations in either of the two transport systems. Complementation tests revealed only one gene, araE, in the low-affinity arabinose uptake system. P1 transduction placed araE between lysA (60.9 min) and thyA (60.5 min) and closer to lysA. The operon of the high-affinity transport system was found to contain two genes: araF, which codes for the arabinose-binding protein, and a new gene, araG. The newly identified gene, araG, was shown by two-dimensional gel electrophoresis to encode a protein which is located in the membrane. Only defects in araG could abolish uptake by the high-affinity system under the conditions we used.
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36
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37
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Clark AF, Hogg RW. High-affinity arabinose transport mutants of Escherichia coli: isolation and gene location. J Bacteriol 1981; 147:920-4. [PMID: 7024251 PMCID: PMC216128 DOI: 10.1128/jb.147.3.920-924.1981] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The gene araF, the product of which is the L-arabinose-binding protein--a component of the high-affinity L-arabinose transport system, was located on the Escherichia coli linkage map at 45 min. We established this location using bacteriophage P2 eductates and bacteriophage P1 cotransduction frequencies with the adjacent genetic loci, his (histidine biosynthesis) and mgl (methylgalactoside transport). In addition, we isolated a number of mutants that phenotypically exhibited altered high-affinity L-arabinose transport capacities. At least two of these mutations were located in the araF gene, as binding protein purified from these strains exhibited altered in vitro arabinose-binding properties.
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38
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Enequist HG, Hirst TR, Harayama S, Hardy SJ, Randall LL. Energy is required for maturation of exported proteins in Escherichia coli. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 116:227-33. [PMID: 7018904 DOI: 10.1111/j.1432-1033.1981.tb05323.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
It has been established in numerous cases that proteins which are exported from Escherichia coli are synthesized on membrane-bound polysomes in precursor forms which are proteolytically cleaved to generate the mature species. Here we present evidence that at least one step in the export of proteins requires energy. Energy requirements for processing of the precursors of both the M13 coat protein [Date, T., Zwizinski, C., Ludmerer, S., and Wickner, W. (1980) Proc. Natl Acad. Sci. USA, 77, 827-831; Date, T., Goodman, J. M., and Wickner, W. T. (1980) Proc. Natl Acad. Sci. USA, 77, 4669-4673] and the B subunit of heat-labile enterotoxin [Palva, T., Hirst, T. R., Hardy, S. J. S., Holmgren, J., and Randall, L. L. (1981) J. Bacteriol. in the press] have been demonstrated previously. An energy requirement for the proteolytic processing of an additional five exported proteins is reported here. Studies utilizing an uncA mutant suggest that the form of energy required is proton-motive force. Thus an energized membrane is probably essential for export of most periplasmic and outer membrane proteins.
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39
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MacPherson AJ, Jones-Mortimer MC, Henderson PJ. Identification of the AraE transport protein of Escherichia coli. Biochem J 1981; 196:269-83. [PMID: 7030324 PMCID: PMC1162991 DOI: 10.1042/bj1960269] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
1. Two arabinose-inducible proteins are detected in membrane preparations from strains of Escherichia coli containing arabinose-H+ (or fucose-H+) transport activity; one protein has an apparent subunit relative molecular mass (Mr) of 36 000-37 000 and the other has Mr 27 000. 2. An araE deletion mutant was isolated and characterized; it has lost arabinose-H+ symport activity and the arabinose-inducible protein of Mr 36 000, but not the protein of Mr 27 000. 3. An araE+ specialized transducing phage was characterized and used to re-introduce the araE+ gene into the deletion strain, a procedure that restores both arabinose-H+ symport activity and the protein of Mr 36,000. 4. N-Ethylmaleimide inhibits arabinose transport and partially inhibits arabinose-H+ symport activity. 5. N-Ethylmaleimide modifies an arabinose-inducible protein of Mr 36 000-38 000, and arabinose protects the protein against the reagent. 6. These observations identify an arabinose-transport protein of Escherichia coli as the product of the araE+ gene. 7. The protein was recognized as a single spot staining with Coomassie Blue after two-dimensional gel electrophoresis.
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40
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Lazzaroni JC, Portalier RC. Genetic and biochemical characterization of periplasmic-leaky mutants of Escherichia coli K-12. J Bacteriol 1981; 145:1351-8. [PMID: 7009581 PMCID: PMC217139 DOI: 10.1128/jb.145.3.1351-1358.1981] [Citation(s) in RCA: 112] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Periplasmic-leaky mutants of Escherichia coli K-12 were isolated after nitrosoguanidine-induced mutagenesis. They released periplasmic enzymes into the extracellular medium. Excretion of alkaline phosphatase, which started immediately in the early exponential phase of growth, could reach up to 90% of the total enzyme production in the stationary phase. Leaky mutants were sensitive to ethylenediaminetetraacetic acid, cholic acid, and the antibiotics rifampin, chloramphenicol, mitomycin C, and ampicillin. Furthermore, they were resistant to colicin E1 and partially resistant to phage TuLa. Their genetic characterization showed that the lky mutations mapped between the suc and gal markers, near or in the tolPAB locus. A biochemical analysis of cell envelope components showed that periplasmic-leaky mutants contained reduced amounts of major outer membrane protein OmpF and increased amounts of a 16,000-dalton outer membrane protein.
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41
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42
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Iuchi S, Tanaka S. Catabolite-like repression of extracellular enzyme production in Vibrio parahaemolyticus. Microbiol Immunol 1980; 24:803-14. [PMID: 6163949 DOI: 10.1111/j.1348-0421.1980.tb02885.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Production of extracellular amylase and protease in Vibrio parahaemolyticus was repressed by various carbohydrates present in the medium. In addition, the protease production was repressed very strongly by peptones or casamino acids. Cyclic adenosine 3', 5'-monophosphate (cyclic AMP) added exogenously could reverse the repression of amylase production, but not that of protease production irrespective of the "repressors" used. Mutants of V. parahaemolyticus, which resembled the reported cya (adenylate cyclase) and crp (cyclic AMP receptor protein) mutants of Escherichia coli and related organisms, were examined for the exoenzyme production. Amylase production in the mutants was defective, while their protease production was not defective, but rather accentuated as compared with that in the parental strain. These findings strongly suggest that amylase production is subject to catabolite repression mediated by cyclic AMP, whereas protease production is controlled by a repression mechanism which mimics in part, but may be distinct from catabolite repression.
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43
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The thiol group of the L-arabinose-binding protein. Chromophoric labeling and chemical identification of the sugar-binding site. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)35975-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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44
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Abstract
Salmonella typhimurium LT2 grows on D-xylose as sole carbon source with a generation time of 105 to 110 min. The following activities are induced at the indicated time after the addition of the inducer, D-xylose: D-xylulokinase (5 min), D-xylose isomerase (7 to 8 min), and D-xylose transport (10 min). All other pentoses and pentitols tested failed to induce isomerase or kinase. Synthesis of D-xylose isomerase was subject to catabolite repression, which was reversed by the addition of cyclic adenosine monophosphate. Most of the radioactive counts from D-[14C]xylose were initially accumulated in the cell in the form of D-xylose or D-xylulose. D-Xylose uptake in a mutant which was deficient in D-xylose isomerase was equal to that of the wild type. The apparent Km for D-xylose uptake was 0.41 mM. Some L-arabinose was accumulated in D-xylose-induced cells, and some D-xylose was accumulated in L-arabinose-induced cells. D-Xylitol and L-arabinose competed against C-xylose uptake, but D-arabinose, D-lyxose, and L-lyxose did not. Osmotic shock reduced the uptake of D-xylose by about 50%; by equilibrium dialysis, a D-xylose-binding protein was detected in the supernatant fluid after spheroplasts were formed from D-xylose-induced cells.
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45
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Marty B, Gaudin C, Ragot M, Belaich A, Belaích JP. Microcalorimetric study of glutamine fixation on the glutamine-binding protein of Escherichia coli. Biochem Biophys Res Commun 1979; 86:1118-25. [PMID: 373759 DOI: 10.1016/0006-291x(79)90233-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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46
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Howe MM, Schumm JW, Taylor AL. The S and U genes of bacteriophage mu are located in the invertible G segment of mu DNA. Virology 1979; 92:108-24. [PMID: 419685 DOI: 10.1016/0042-6822(79)90218-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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47
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Randall LL, Josefsson LG, Hardy SJ. Processing in vitro of precursor periplasmic proteins from Escherichia coli. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 92:411-5. [PMID: 367780 DOI: 10.1111/j.1432-1033.1978.tb12761.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Precursors of two secreted periplasmic proteins in Escherichia coli, arabinose-binding protein and maltose-binding protein, were synthesized in vitro on membrane-bound polysomes. Addition of Triton X-100 to the system resulted in processing of the precursors to mature forms.
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48
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Steffen D, Schleif R. Overproducing araC protein with lambda-arabinose transducing phage. MOLECULAR & GENERAL GENETICS : MGG 1977; 157:333-9. [PMID: 340930 DOI: 10.1007/bf00268671] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Escherichia coli infected with bacteriophage lambda-arabinose transducing phage were tested as sources of araC protein. Infection of cells with such phage produces an intracellular concentration of araC protein up to 100 times that present in wild-type E. coli, apparently resulting from fusion of the araC gene to bacteriophage lambda promoters. Lysates from these phage-infected cells may be fractionated to yield another 100-fold enrichment in araC activity so that the total enrichment is 10,000-fold. A nonsense mutation in araC provided proof of the identification on gel electrophoresis of a band in the purified material. Biologically active araC protein is a dimer with 28,000 M.W. subunits. The araC gene in these phage replaces the int-xis genes but is oriented in the opposite direction. Nonetheless, it appears to be transcribed in this position by the phage promoter pr via transcription the long way around. Furthermore, because araC gene is in this position, we were able to isolate phage on which the araC gene was under phage late gene control by deletion of the late gene transcription stop signals in the b2 region.
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49
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Steffen D, Schleif R. In vitro construction of plasmids which result in overproduction of the protein product of the araC gene of Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1977; 157:341-4. [PMID: 340931 DOI: 10.1007/bf00268672] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Derivatives of the Escherichia coli drug resistance plasmid pMB-9 were constructed which contain the promoter from the lactose operon of E. coli fused to the araC gene of E. coli. E. coli possessing these plasmids contain about 50 times as much of the araC gene product as do cells with a wild-type araC gene and promotor.
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Abstract
The start sites of the araC and araBAD gene messenger of E. coli were located by transcription in vitro from short DNA fragments, by high magnification electron microscopy and by genetic mapping. Transcription for these messengers proceeds in opposite directions from the start sites that are 150 base pairs apart. Transcription from the araBAD promoter requires araC protein plus arabinose and CAP protein plus cyclic AMP. In the experiments performed in vitro, inducing the araBAD promoter represses activity of the araC promoter.
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