Regulatory proteins and cis-acting elements involved in the transcriptional control of Rhizobium etli reiterated nifH genes.

ABSTRACTCyanobacteria have evolved a suite of enzymes and inorganic carbon (Ci) transporters that improve photosynthetic performance by increasing the localized concentration of CO2 around the primary CO2-fixating enzyme, Rubisco. This CO2-concentrating mechanism (CCM) is highly regulated, responds to illumination/darkness cycles and allows cyanobacteria to thrive under limiting Ci conditions. While the transcriptional control of CCM activity is well understood, less is known about how regulatory proteins might allosterically regulate Ci transporters in response to changing conditions. Cyanobacterial sodium-dependent bicarbonate transporters (SbtAs) are inhibited by PII-like regulatory proteins (SbtBs), with the inhibitory effect being modulated by adenylnucleotides. Here, we used isothermal titration calorimetry to show that SbtB from Cyanobium sp. PCC7001 (SbtB7001) binds AMP, ADP, cAMP and ATP with micromolar-range affinities. X-ray crystal structures of apo- and nucleotide-bound SbtB7001 revealed that while AMP, ADP and cAMP have little effect on the SbtB7001 structure, binding of ATP stabilizes the otherwise flexible T-loop and that the flexible C-terminal C-loop adopts several distinct conformations. We also show that ATP binding affinity is increased ten-fold in the presence of Ca2+ and we present an X-ray crystal structure of Ca2+ATP:SbtB7001 that shows how this metal ion facilitates additional stabilizing interactions with the apex of the T-loop. We propose that the Ca2+ATP-induced conformational change observed in SbtB7001 is important for allosteric regulation of SbtA activity by SbtB and is consistent with changing adenylnucleotide levels in illumination/darkness cycles.GRAPHICAL ABSTRACT

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Symbiosis-Specific Transcriptional Control of Rhizobium etli Rpon2

Nitrogen Fixation: From Molecules to Crop Productivity - Current Plant Science and Biotechnology in Agriculture ◽

10.1007/0-306-47615-0_73 ◽

2005 ◽

pp. 140-140

Author(s):

B. Dombrecht ◽

J. Michiels ◽

J. Vanderleyden

Keyword(s):

Transcriptional Control ◽

Rhizobium Etli

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Localization and Interaction of the Proteins Constituting the GAL Genetic Switch in Saccharomyces cerevisiae

Eukaryotic Cell ◽

10.1128/ec.00261-08 ◽

2008 ◽

Vol 7 (12) ◽

pp. 2061-2068 ◽

Cited By ~ 22

Author(s):

Raymond Wightman ◽

Rachel Bell ◽

Richard J. Reece

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Cellular Localization ◽

Transcriptional Control ◽

Resonance Energy ◽

Regulatory Proteins ◽

Yeast Cells ◽

Galactose Metabolism ◽

Genetic Switch ◽

Metabolism Regulation

ABSTRACT In Saccharomyces cerevisiae, the GAL genes encode the enzymes required for galactose metabolism. Regulation of these genes has served as the paradigm for eukaryotic transcriptional control over the last 50 years. The switch between inert and active gene expression is dependent upon three proteins—the transcriptional activator Gal4p, the inhibitor Gal80p, and the ligand sensor Gal3p. Here, we present a detailed spatial analysis of the three GAL regulatory proteins produced from their native genomic loci. Using a novel application of photobleaching, we demonstrate, for the first time, that the Gal3p ligand sensor enters the nucleus of yeast cells in the presence of galactose. Additionally, using Förster resonance energy transfer, we show that the interaction between Gal3p and Gal80p occurs throughout the yeast cell. Taken together, these data challenge existing models for the cellular localization of the regulatory proteins during the induction of GAL gene expression by galactose and suggest a mechanism for the induction of the GAL genes in which galactose-bound Gal3p moves from the cytoplasm to the nucleus to interact with the transcriptional inhibitor Gal80p.

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The Relaxase of the Rhizobium etli Symbiotic Plasmid Shows nic Site cis-Acting Preference

Journal of Bacteriology ◽

10.1128/jb.00701-06 ◽

2006 ◽

Vol 188 (21) ◽

pp. 7488-7499 ◽

Cited By ~ 16

Author(s):

Daniel Pérez-Mendoza ◽

María Lucas ◽

Socorro Muñoz ◽

José A. Herrera-Cervera ◽

José Olivares ◽

...

Keyword(s):

Biochemical Characterization ◽

Rhizobium Etli ◽

Cis Acting ◽

Cleavage Activity ◽

Symbiotic Plasmid ◽

The Family ◽

Nick Site ◽

First Time

ABSTRACT Genetic and biochemical characterization of TraA, the relaxase of symbiotic plasmid pRetCFN42d from Rhizobium etli, is described. After purifying the relaxase domain (N265TraA), we demonstrated nic binding and cleavage activity in vitro and thus characterized for the first time the nick site (nic) of a plasmid in the family Rhizobiaceae. We studied the range of N265TraA relaxase specificity in vitro by testing different oligonucleotides in binding and nicking assays. In addition, the ability of pRetCFN42d to mobilize different Rhizobiaceae plasmid origins of transfer (oriT) was examined. Data obtained with these approaches allowed us to establish functional and phylogenetic relationships between different plasmids of this family. Our results suggest novel characteristics of the R. etli pSym relaxase for previously described conjugative systems, with emphasis on the oriT cis-acting preference of this enzyme and its possible biological relevance.

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ON THE NATURE OF CIS-ACTING REGULATORY PROTEINS AND GENETIC ORGANIZATION IN BACTERIOPHAGE: THE EXAMPLE OF GENE Q OF BACTERIOPHAGE Λ

Genetics ◽

10.1093/genetics/83.1.5 ◽

1976 ◽

Vol 83 (1) ◽

pp. 5-10

Author(s):

Harrison Echols ◽

Donald Court ◽

Linda Green

Keyword(s):

Dna Binding ◽

Regulatory Protein ◽

Dna Binding Protein ◽

Regulatory Proteins ◽

Bacteriophage Λ ◽

Complete Spectrum ◽

Cis Acting ◽

Nonspecific Interactions ◽

Q Gene ◽

Linkage Of Genes

ABSTRACT We note the existence of a "partially cis-acting" regulatory protein of bacteriophage λ: the product of the phage Q gene. We suggest that there may be a complete spectrum from "all cis" to "all trans" for such regulatory proteins. This behavior might arise because a DNA-binding protein either acts at a nearby (cis) site soon after synthesis or becomes "lost" for its trans activity on another genome through nonspecific interactions with DNA. Our proposed explanation provides one evolutionary basis for the linkage of genes for regulatory proteins and the sites at which such proteins act; it also suggests a possible rationale for the "metabolic instability" of certain regulatory proteins.

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cis-Acting Elements Responsible for Low-Temperature-Inducible Expression of the Gene Coding for the Thermolabile Isocitrate Dehydrogenase Isozyme of a Psychrophilic Bacterium, Vibrio sp. Strain ABE-1

Journal of Bacteriology ◽

10.1128/jb.181.8.2602-2611.1999 ◽

1999 ◽

Vol 181 (8) ◽

pp. 2602-2611 ◽

Cited By ~ 13

Author(s):

Takehiko Sahara ◽

Masahiro Suzuki ◽

Jun-Ichiro Tsuruha ◽

Yasuhiro Takada ◽

Noriyuki Fukunaga

Keyword(s):

Low Temperature ◽

Isocitrate Dehydrogenase ◽

Transcriptional Control ◽

Fusion Gene ◽

Inducible Expression ◽

Psychrophilic Bacterium ◽

Gene Encoding ◽

Reading Frame ◽

Cis Acting ◽

Dehydrogenase Isozyme

ABSTRACT Transcriptional control of the low-temperature-inducibleicdII gene, encoding the thermolabile isocitrate dehydrogenase of a psychrophilic bacterium, Vibrio sp. strain ABE-1, was found to be mediated in part by a transcriptional silencer locating at nucleotide positions −560 to −526 upstream from the transcription start site of icdII. Deletion of the silencer resulted in a 20-fold-increased level of expression of the gene at low temperature (15°C) but not at high temperature (37°C). In addition, a CCAAT sequence located 2 bases upstream of the −35 region was found to be essential for the low-temperature-inducible expression of the gene. By deletion of this sequence, low-temperature-dependent expression of the gene was completely abolished. The ability of the icdII promoter to control the expression of other genes was confirmed by using a fusion gene containing the icdII promoter region and the promoterlessicdI open reading frame, which encodes the non-cold-inducible isocitrate dehydrogenase isozyme ofVibrio sp. strain ABE-1. Escherichia colitransformants harboring icdII acquired an ability to grow rapidly at low temperature.

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Cell-type-dependent gene activation by yeast transposon Ty1 involves multiple regulatory determinants

Molecular and Cellular Biology ◽

10.1128/mcb.7.9.3205-3211.1987 ◽

1987 ◽

Vol 7 (9) ◽

pp. 3205-3211

Author(s):

M Company ◽

B Errede

Keyword(s):

Gene Expression ◽

Transcriptional Control ◽

Gene Activation ◽

Distal Region ◽

Control Site ◽

Cell Type ◽

Cell Type Specificity ◽

Negative Effects ◽

Cis Acting ◽

Transcriptional Control Region

Ty transposable element insertion mutations of Saccharomyces cerevisiae can cause cell-type-dependent activation of adjacent gene expression. Several cis-acting regulatory regions within Ty1 that are responsible for these effects were identified. A 211-base-pair (bp) region functions as an activator. This region includes the so-called U5 domain of delta and 145 bp of adjacent epsilon sequences. Unlike activation by the intact Ty1, activation by the 211-bp Ty1 subfragment is cell-type independent. The presence of a 112-bp fragment from a more distal region of Ty1 confers cell-type specificity to the activator. The 112-bp fragment includes sequences with homology to mammalian enhancers and to a yeast a/alpha control site. In addition, Ty1 regions that exert negative effects on gene expression were identified. These results demonstrate that the Ty1 transcriptional control region consists of multiple components with distinct regulatory functions.

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Evolutionary conservation of homeodomain-binding sites and other sequences upstream and within the major transcription unit of the Drosophila segmentation gene engrailed

Molecular and Cellular Biology ◽

10.1128/mcb.9.10.4304-4311.1989 ◽

1989 ◽

Vol 9 (10) ◽

pp. 4304-4311

Author(s):

J A Kassis ◽

C Desplan ◽

D K Wright ◽

P H O'Farrell

Keyword(s):

Binding Sites ◽

Regulatory Region ◽

Divergence Time ◽

Evolutionary Conservation ◽

Transcription Unit ◽

Regulatory Proteins ◽

Coding Region ◽

Cis Acting ◽

Perfect Sequence ◽

Development Proceeds

The engrailed (en) gene functions throughout Drosophila development and is expressed in a succession of intricate spatial patterns as development proceeds. Normal en function relies on an extremely large cis-acting regulatory region (70 kilobases). We are using evolutionary conservation to help identify en sequences important in regulating patterned expression. Sequence comparison of 2.6 kilobases upstream of the en coding region of D. melanogaster and D. virilis (estimated divergence time, 60 million years) showed that 30% of this DNA occurs in islands of near perfect sequence conservation. One of these conserved islands contains binding sites for homeodomain-containing proteins. It has been shown genetically that homeodomain-containing proteins regulate en expression. Our data suggested that this regulation may be direct. The remaining conserved islands may contain binding sites for other regulatory proteins.

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