Repressor Proteins
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- Chapter [8] http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://pub2web.metastore.ingenta.com/ns/Chapter
- Article [2] http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://pub2web.metastore.ingenta.com/ns/Article
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10 results
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Bacteriophages at the Poles
- Author: Robert V. Miller
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Source: Polar Microbiology: Life in a Deep Freeze , pp 62-78
Publication Date :
January 2012
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Abstract:
This chapter explores the data collected on the importance of bacteriophages to the ecology of the earth's polar regions. It examines the numbers of phage-like particles that have been observed in the ecosystems and their importance in regulating bacterial numbers and the food chain of the extreme oligotrophic environments. To understand the potential impact of bacteriophages on polar ecosystems, it is first necessary to understand the different life choices of phages and how environmental factors are known to affect them. Perhaps not surprisingly, these data suggest that bacteriophages are an important shunt in carbon cycling in the Antarctic regions as well as in the Arctic. Unlike many other studies, the authors conclude that neither bacteriovores nor bacteriophages are important regulators of bacterial numbers but that numbers are regulated by algae blooms and other factors that affect bacterial growth. Pseudolysogeny was first defined by Baess in 1971. In his review, pseudolysogeny was identified as a phage-host interaction in which the phage, following infection of the host, elicits an unstable, nonproductive response. Thus any study that enumerates total virus-like particles (VLPs) must be tempered with the understanding that not all will be infective. The data obtained in this study support the hypothesis that bacteriophages are of quantifiable significance in the carbon-flow cycle of Antarctic oligotrophic lakes. Few researchers have investigated bacteriophages in both the Arctic and Antarctic in the same study. Phylogenetic analysis of their data revealed five previously uncharacterized subgroups of T4-like bacteriophages in many environments, including the Arctic samples.
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A Small Group Activity About Bacterial Regulation And Complementation †
- Authors: Susan Merkel*, Buck Hanson, Adam Parks
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Citation: Merkel S, Hanson B, Parks A. 2010. A small group activity about bacterial regulation and complementation † . 11(2):152-155 doi:10.1128/jmbe.v11i2.196
- DOI 10.1128/jmbe.v11i2.196
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Abstract:
As teachers, we well understand the need for activities that help develop critical-thinking skills in microbiology. In our experience, one concept that students have difficulty understanding is transcriptional regulation of bacterial genes. To help with this, we developed and evaluated a paper-based activity to help students understand and apply the concepts of bacterial transcriptional regulation. While we don’t identify it as such, we use a complementation experiment to assess student understanding of how regulation changes when new DNA is introduced. In Part 1 of this activity, students complete an open-book, take-home assignment that asks them to define common terminology related to regulation, and draw the regulatory components of different scenarios involving positive and negative regulation. In Part 2, students work in small groups of 3–4 to depict the regulatory components for a different scenario. They are asked to explain the results of a complementation experiment based on this scenario. They then predict the results of a slightly different experiment. Students who completed the Regulation Activity did significantly better on post-test questions related to regulation, compared to pre-test questions.
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Promoter Escape by Escherichia coli RNA Polymerase
- Author: Lilian M. Hsu
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Citation: Hsu L. 2008. Promoter Escape by Escherichia coli RNA Polymerase, EcoSal Plus 2008; doi:10.1128/ecosalplus.4.5.2.2
- DOI 10.1128/ecosalplus.4.5.2.2
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Abstract:
Promoter escape is the process that an initiated RNA polymerase (RNAP) molecule undergoes to achieve the initiation-elongation transition. Having made this transition, an RNAP molecule would be relinquished from its promoter hold to perform productive (full-length) transcription. Prior to the transition, this process is accompanied by abortive RNA formation—the amount and pattern of which is controlled by the promoter sequence information. Qualitative and quantitative analysis of abortive/productive transcription from several Escherichia coli promoters and their sequence variants led to the understanding that a strong (RNAP-binding) promoter is more likely to be rate limited (during transcription initiation) at the escape step and produce abortive transcripts. Of the two subelements in a promoter, the PRR (the core Promoter Recognition Region) was found to set the initiation frequency and the rate-limiting step, while the ITS (the Initial Transcribed Sequence region) modulated the ratio of abortive versus productive transcription. The highly abortive behavior of E. coli RNAP could be ameliorated by the presence of Gre (transcript cleavage stimulatory) factor(s), linking the first step in abortive RNA formation by the initial transcribing complexes (ITC) to RNAP backtracking. The discovery that translocation during the initiation stage occurs via DNA scrunching provided the source of energy that converts each ITC into a highly unstable "stressed intermediate." Mapping all of the biochemical information onto an X-ray crystallographic structural model of an open complex gave rise to a plausible mechanism of transcription initiation. The chapter concludes with contemplations of the kinetics and thermodynamics of abortive initiation-promoter escape.
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Cells Respond to Their External Environments
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Source: Biology and Biotechnology , pp 157-182
Publication Date :
January 2005
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This chapter discusses the types of cell signals and cell receptors, examples of direct interaction between the environment and single-celled organisms, how hormones regulate the environment within multicellular organisms regulation of glucose concentration in the blood, regulation of salt and water balance and blood pressure. A key concept for the chapter is that in order for a cell (or, by extension, a multicellular organism) to respond to signals from the environment, all the steps from the signal to the effect must be in place. The chapter discusses some examples of cascades related to some of the ways our bodies regulate salt and water balance. Some basics of signaling and response are illustrated by an example from the bacterium Escherichia coli. The interconnected system of hormones that regulate body’s blood pressure and salt and water balance, and the major hormones involved in blood pressure regulation are explained. Each of these hormones has a receptor through which it exerts its effects. Taking diabetes as an example, one might assume that blood pressure regulation could be impaired by either a failure to make one of the hormones or a failure to respond to it. Kidney failure is treated with dialysis, in which blood is pumped through porous membrane tubes suspended in fluid containing healthy concentrations of salt and glucose.
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Permeability as an Excuse to Write What I Feel
- Author: Georges N. Cohen
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Source: Origins of Molecular Biology , pp 109-116
Publication Date :
January 2003
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This chapter states that initial rates of β-galactosidase production were very similar with and without inducer. The author thinks it is safe to say that this PaJaMa experiment provided the basis and frame of reference for further studies on the mechanism of enzyme regulation. The PaJaMa experiment is the basis of a historical-philosophical study of the nature of discovery by Kenneth Schaffner, who interviewed the individuals involved and reconstructed a composite of what happened. From the PaJaMa studies on the molecular nature of induction—proposed to be the effects of interaction of a lactose-related inducer with the repressor protein, which initiates a quite different process of gene expression—Jacques Monod became interested in how a small molecule can modify a protein’s function. The author says that the time spent by him in Monod’s laboratory was certainly one of the most remarkable of his career, as he learned there of the great power of genetics in combination with biochemistry.
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The PaJaMa Experiment
- Author: Arthur B. Pardee
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Source: Origins of Molecular Biology , pp 133-142
Publication Date :
January 2003
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The author undertook a systematic screening of the inducing capacity of all available thiogalactosides, of their affinity to the purified β-galactosidase, and of their “apparent affinity” to the intracellular enzyme. Constitutive strains, which synthesized β-galactosidase in media devoid of inducer, had been isolated. The prevailing hypothesis was that they accumulated an “internal” inducer. The availability of powerful inhibitors of induction prompted the author's group to check their ability to block the constitutive synthesis, with entirely negative results. The author attempted to map the operator gene. The bias was that the strains utilized were heterogeneous in the activity of a galactose transport system. The operator moved back to one end of the galactose operon. The striking similarity exhibited by the regulatory elements of the lactose and galactose systems strengthened both the repressor hypothesis and the notion that the unit of genetic expression can comprise several genes. Taking advantage of the fact that the lactose regulator gene i is close enough to the genes it controls to also remain associated to them in the transducing phages, Salvador Luria could establish that the cointegration of an active i gene was necessary and sufficient to prevent the derepression of the lactose enzymes during the phage vegetative growth. Unfortunately, the structure of the galactose system did not enable one to decide if the same explanation accounted entirely for the derepression of galactokinase. The switch "from lactose to galactose" induction analysis also supplied unexpected insights on the deregulation of host enzyme synthesis by viral induction.
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From Diauxie to the Concept of Catabolite Repression
- Author: Boris Magasanik
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Source: Origins of Molecular Biology , pp 169-174
Publication Date :
January 2003
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Abstract:
The most universally known and the most often misquoted is "Whatever is true for E. coli is true for an elephant." Jacques Monod's faith in the universality of the laws and mechanisms of biology contrasting with his provocative attitude of apparent cynicism in front of the great problems of "the secrets of life" was fascinating to those of us who surrounded him. Monod showed with Melvin Cohn that the kinetic parameters as well as the immunochemical properties of β-galactosidase did not change when a variety of inducers were utilized with the inducible strain or compared to the enzyme of the constitutive mutants, where no inducer was used. The rapid regulatory switches pointed toward an unstable intermediate embodying the genetic information between gene and protein. The intermediate, called "the messenger," soon became the messenger RNA, (mRNA). The progress of translation is independent of both the termination of the transcription and the survival of the initial end of mRNA. The survival of the initiating end of mRNA is independent of the intracellular concentration of inducer and largely, although not completely, independent of transcription. The mRNA is polycistronic and stays probably as a single piece for the major part of its functional lifetime. At the steady state of all processes, the polycistronic mRNA is, however, seldom integral. The major part of it should be pieces: some unfinished, some already missing the initiating end, some devoid of both, still growing on one side while losing the other side at the same speed.
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Nitrogen Source Utilization and Its Regulation
- Authors: Susan H. Fisher, Michel Débarbouillé
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Source: Bacillus subtilis and Its Closest Relatives , pp 181-191
Publication Date :
January 2002
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In Bacillus subtilis and other gram-positive bacteria, nitrogen metabolism genes are regulated by fundamentally different mechanisms. Three proteins—GlnR, TnrA, and CodY—control gene expression in response to nitrogen availability in B. subtilis. TnrA both activates and represses transcription during nitrogen-limited growth. TnrA-like proteins have been identified by sequence analysis in B. stearotfiermophilus and B. halodurans. Four nitrogen degradative pathways—arginine, histidine, glutamate and urea—are described in this chapter. By several criteria, glutamine serves as the best nitrogen source for B. subtilis, followed by arginine. The regulation and genetics of several nitrogen catabolite pathways are also discussed in the chapter. B. Iicheniformis has two routes for arginine degradation, the arginase-dependent and arginine deiminase-dependent pathways. Expression of both pathways is induced by arginine and repressed by growth in the presence of glucose. Expression of the B. subtilis histidine-degrading enzymes is induced by histidine and subject to nutritional regulation by CodY and CcpA. The expression of the plasmid-encoded ure genes found in several Clostridium perfringens strains and the chromosomal ure genes in B. subtilis are nitrogen regulated. Several low-G+C gram-positive bacteria contain genes encoding NrgA-like ammonium transporters proteins. The second gene in the B. subtilis nrgAB operon encodes a protein that resembles the PII signal transduction protein found in the enteric Ntr nitrogen regulatory system and in cyanobacteria.
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Intercellular Communication in Marine Vibrio Species: Density-Dependent Regulation of the Expression of Bioluminescence
- Authors: Bonnie L. Bassler, Michael R. Silverman
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Source: Two-Component Signal Transduction , pp 431-445
Publication Date :
January 1995
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This chapter focuses on the different molecular mechanisms two model luminous bacteria, Vibrio fischeri (a symbiont) and V. harveyi (a free-living microbe), use for regulating lux expression. Expression of luminescence in most bacteria is tightly regulated by the density of the population. In V. fischeri, the regulatory genes involved in density-dependent control of luminescence are adjacent to the luxCDABEG operon encoding the luciferase enzymes. The regulatory genes that control luminescence in V. harveyi are different from those of V. fischeri. One complementation group of V. harveyi dim mutants could be restored to full light production by a family of recombinant cosmids containing a subset of common restriction fragments. Initial HAI-1 and HAI-2 signal recognition by LuxN and LuxQ could activate a series of phosphotransfer reactions. Two-component circuits have been characterized in which a single protein contains both a sensor kinase and a response regulator domain (similar to LuxN and LuxQ) and a second protein contains both a response regulator domain and a DNA binding motif (similar to LuxO). The differences between the regulatory circuits controlling density-dependent expression of luminescence in V. fischeri and V. harveyi are striking. Subsequent mutations and gene duplications and rearrangements generated new and multiple autoinducers, receptivities, and regulatory connections, finally resulting in a bacterium with the properties of V. harveyi.
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Utilization of Amino Acids and Other Nitrogen-Containing Compounds
- Author: Susan H. Fisher
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Source: Bacillus subtilis and Other Gram-Positive Bacteria , pp 221-228
Publication Date :
January 1993
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This chapter discusses the catabolism of amino acids and other nitrogen-containing compounds. Aspartate is transported into B. subtilis by two systems, a high-affinity system energized by the proton motive force and a low-affinity system. The enzymes of the arginase degradative pathway are found in B. subtilis and B. licheniformis. In B. subtilis and B. licheniformis, the proline-degradative enzymes are induced by proline. In B. subtilis, this induction is inhibited if the growth medium also contains glucose and amino acids. Hut expression in B. subtilis is induced by histidine and repressed by rapidly metabolized carbon sources such as glucose. Growth in the presence of amino acids severely inhibits synthesis of the Hut enzymes. Dehydrogenase enzymes may play a role in the degradation of phenylalanine in Bacillus badius, of valine in Streptomyces spp, and of leucine in B. cereus. Nitrate reductase activity is found in B. subtilis cells growing in the presence of nitrate under semianaerobic conditions. Amino acids and small peptides produced by the degradation of extracellular polypeptides can also supply B. subtilis with nutrients during growth and sporulation.