Transcriptional Regulation of the pdt Gene Cluster of Pseudomonas stutzeri KC Involves an AraC/XylS Family Transcriptional Activator (PdtC) and the Cognate Siderophore Pyridine-2,6-Bis(Thiocarboxylic Acid)

ABSTRACT In order to gain an understanding of the molecular mechanisms dictating production of the siderophore and dechlorination agent pyridine-2,6-bis(thiocarboxylic acid) (PDTC), we have begun characterization of a gene found in the pdt gene cluster of Pseudomonas stutzeri KC predicted to have a regulatory role. That gene product is an AraC family transcriptional activator, PdtC. Quantitative reverse transcription-PCR and expression of transcriptional reporter fusions were used to assess a role for pdtC in the transcription of pdt genes. PdtC and an upstream, promoter-proximal DNA segment were required for wild-type levels of expression from the promoter of a predicted biosynthesis operon (P pdt F ). At least two other transcriptional units within the pdt cluster were also dependent upon pdtC for expression at wild-type levels. The use of a heterologous, Pseudomonas putida host demonstrated that pdtC and an exogenously added siderophore were necessary and sufficient for expression from the pdtF promoter, i.e., none of the PDTC utilization genes within the pdt cluster were required for transcriptional signaling. Tests using the promoter of the pdtC gene in transcriptional reporter fusions indicated siderophore-dependent negative autoregulation similar to that seen with other AraC-type regulators of siderophore biosynthesis and utilization genes. The data increase the repertoire of siderophore systems known to be regulated by this type of transcriptional activator and have implications for PDTC signaling.

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A Pseudomonas stutzeri gene cluster encoding the biosynthesis of the CCl4-dechlorination agent pyridine-2,6-bis(thiocarboxylic acid)

Environmental Microbiology ◽

10.1046/j.1462-2920.2000.00122.x ◽

2000 ◽

Vol 2 (4) ◽

pp. 407-416 ◽

Cited By ~ 42

Author(s):

Thomas A. Lewis ◽

Marc S. Cortese ◽

Jonathan L. Sebat ◽

Tonia L. Green ◽

Chang-Ho Lee ◽

...

Keyword(s):

Gene Cluster ◽

Pseudomonas Stutzeri ◽

Thiocarboxylic Acid

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Pyridine-2,6-Bis(Thiocarboxylic Acid) Produced by Pseudomonas stutzeri KC Reduces and Precipitates Selenium and Tellurium Oxyanions

Applied and Environmental Microbiology ◽

10.1128/aem.72.5.3119-3129.2006 ◽

2006 ◽

Vol 72 (5) ◽

pp. 3119-3129 ◽

Cited By ~ 33

Author(s):

Anna M. Zawadzka ◽

Ronald L. Crawford ◽

Andrzej J. Paszczynski

Keyword(s):

Wild Type Strain ◽

Hydrolysis Product ◽

Pseudomonas Stutzeri ◽

Elemental Selenium ◽

Bacterial Cells ◽

Wild Type ◽

Chemical Structures ◽

Thiocarboxylic Acid ◽

Insoluble Compounds ◽

Initial Line

ABSTRACT The siderophore of Pseudomonas stutzeri KC, pyridine-2,6-bis(thiocarboxylic acid) (pdtc), is shown to detoxify selenium and tellurium oxyanions in bacterial cultures. A mechanism for pdtc's detoxification of tellurite and selenite is proposed. The mechanism is based upon determination using mass spectrometry and energy-dispersive X-ray spectrometry of the chemical structures of compounds formed during initial reactions of tellurite and selenite with pdtc. Selenite and tellurite are reduced by pdtc or its hydrolysis product H2S, forming zero-valent pdtc selenides and pdtc tellurides that precipitate from solution. These insoluble compounds then hydrolyze, releasing nanometer-sized particles of elemental selenium or tellurium. Electron microscopy studies showed both extracellular precipitation and internal deposition of these metalloids by bacterial cells. The precipitates formed with synthetic pdtc were similar to those formed in pdtc-producing cultures of P. stutzeri KC. Culture filtrates of P. stutzeri KC containing pdtc were also active in removing selenite and precipitating elemental selenium and tellurium. The pdtc-producing wild-type strain KC conferred higher tolerance against selenite and tellurite toxicity than a pdtc-negative mutant strain, CTN1. These observations support the hypothesis that pdtc not only functions as a siderophore but also is involved in an initial line of defense against toxicity from various metals and metalloids.

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Regulation of RUNX1 Transcriptional Function by GATA-1 Kinase Recruitment: A Novel Pathway for Megakaryocytic Gene Regulation.

Blood ◽

10.1182/blood.v108.11.1183.1183 ◽

2006 ◽

Vol 108 (11) ◽

pp. 1183-1183

Author(s):

Kamaleldin E. Elagib ◽

Ivailo S. Mihaylov ◽

Lorrie L. Delehanty ◽

Sara L. Gonias ◽

Jill F. Caronia ◽

...

Keyword(s):

Transcriptional Activation ◽

Molecular Mechanisms ◽

Wild Type ◽

New Paradigm ◽

Mobility Shift ◽

Biochemical Basis ◽

Cyclin Dependent Kinases ◽

Functional Differences ◽

Two Factors ◽

Necessary And Sufficient

Abstract RUNX1 and GATA-1 both play essential roles in the transcriptional programming of normal mammalian megakaryocytic development, deficiencies of either factor having similar phenotypic consequences. We have previously characterized physical and functional interactions between these two factors, and others have confirmed analogous cooperations in Drosophila and Danio homologs. We now present data on molecular mechanisms for the cooperation of these two factors in the transcriptional activation of the megakaryocytic aIIb integrin promoter. In these studies, GATA-2 also physically interacted with RUNX1 but failed to cooperate in transcriptional activation. In fact, increasing amounts of GATA-2 repressed the functional interplay between GATA-1 and RUNX1. Through generation of GATA-2/GATA-1 chimeras, we identified a conserved subdomain within the GATA-1 amino terminus that was both necessary and sufficient for transcriptional cooperation with RUNX1. Coexpression of wild type GATA-1 or of cooperating GATA-2/GATA-1 chimeras, but not of GATA-2 or of non-cooperating chimeras, induced a mobility shift in wild type RUNX1. Using immunoprecipitation followed by immunoblot with a panel of phosphospecific antibodies, we found GATA-1 to induce RUNX1 phosphorylation at recognition sites for cyclin-dependent kinases (cdks). Treatment of cells with roscovitine, a specific cdk inhibitor, blocked the transcriptional cooperation of GATA-1 with RUNX1 and eliminated the RUNX1 mobility shift caused by GATA-1 coexpression. Mutagenesis of RUNX1 identified a cluster of serine/threonine-proline (S/TP) sites collectively required for the transcriptional augmentation and mobility shift induced by GATA-1. In addition, intact DNA binding by RUNX1 was required for cooperation with GATA-1. These results provide a new paradigm for cooperation of interacting transcription factors, in which one partner recruits a kinase leading to phosphorylation and activation of the other partner. Furthermore, these results provide a biochemical basis for the previously inexplicable functional differences between GATA-1, which promotes megakaryocytic maturation, and GATA-2 which promotes proliferation without maturation.

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Identification and Utility of FdmR1 as a Streptomyces Antibiotic Regulatory Protein Activator for Fredericamycin Production in Streptomyces griseus ATCC 49344 and Heterologous Hosts

Journal of Bacteriology ◽

10.1128/jb.00592-08 ◽

2008 ◽

Vol 190 (16) ◽

pp. 5587-5596 ◽

Cited By ~ 64

Author(s):

Yihua Chen ◽

Evelyn Wendt-Pienkowski ◽

Ben Shen

Keyword(s):

Gene Cluster ◽

Regulatory Protein ◽

Constitutive Expression ◽

Streptomyces Griseus ◽

Biosynthetic Gene Cluster ◽

Positive Control ◽

Wild Type ◽

Reverse Transcription Pcr ◽

Protein Activator ◽

Biosynthetic Machinery

ABSTRACT The fredericamycin (FDM) A biosynthetic gene cluster, cloned previously from Streptomyces griseus ATCC 49344, contains three putative regulatory genes, fdmR, fdmR1, and fdmR2. Their deduced gene products show high similarity to members of the Streptomyces antibiotic regulatory protein (SARP) family (FdmR1) or to MarR-like regulators (FdmR and FdmR2). Here we provide experimental data supporting FdmR1 as a SARP-type activator. Inactivation of fdmR1 abolished FDM biosynthesis, and FDM production could be restored to the fdmR1::aac(3)IV mutant by expressing fdmR1 in trans. Reverse transcription-PCR transcriptional analyses revealed that up to 26 of the 28 genes within the fdm gene cluster, with the exception of fdmR and fdmT2, were under the positive control of FdmR1, directly or indirectly. Overexpression of fdmR1 in S. griseus improved the FDM titer 5.6-fold (to about 1.36 g/liter) relative to that of wild-type S. griseus. Cloning of the complete fdm cluster into an integrative plasmid and subsequent expression in heterologous hosts revealed that considerable amounts of FDMs could be produced in Streptomyces albus but not in Streptomyces lividans. However, the S. lividans host could be engineered to produce FDMs via constitutive expression of fdmR1; FDM production in S. lividans could be enhanced further by overexpressing fdmC, encoding a putative ketoreductase, concomitantly with fdmR1. Taken together, these studies demonstrate the viability of engineering FDM biosynthesis and improving FDM titers in both the native producer S. griseus and heterologous hosts, such as S. albus and S. lividans. The approach taken capitalizes on FdmR1, a key activator of the FDM biosynthetic machinery.

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Molecular Basis of p53 Functional Inactivation by the Leukemic Protein MLL-ELL

Molecular and Cellular Biology ◽

10.1128/mcb.23.12.4230-4246.2003 ◽

2003 ◽

Vol 23 (12) ◽

pp. 4230-4246 ◽

Cited By ~ 32

Author(s):

Dmitri Wiederschain ◽

Hidehiko Kawai ◽

JiJie Gu ◽

Ali Shilatifard ◽

Zhi-Min Yuan

Keyword(s):

Molecular Basis ◽

Molecular Mechanisms ◽

Cellular Transformation ◽

Wild Type ◽

Efficient Inhibitor ◽

C Terminus ◽

Functional Inactivation ◽

Necessary And Sufficient ◽

First Time

ABSTRACT The Eleven Lysine-rich Leukemia (ELL) gene undergoes translocation and fuses in frame to the Multiple Lineage Leukemia (MLL) gene in a substantial proportion of patients suffering from acute forms of leukemia. Molecular mechanisms of cellular transformation by the MLL-ELL fusion are not well understood. Although both MLL-ELL and wild-type ELL can reduce functional activity of p53 tumor suppressor, our data reveal that MLL-ELL is a much more efficient inhibitor of p53 than is wild-type ELL. We also demonstrate for the first time that ELL extreme C terminus [ELL(eCT)] is required for the recruitment of p53 into MLL-ELL nuclear foci and is both necessary and sufficient for the MLL-ELL inhibition of p53-mediated induction of p21 and apoptosis. Finally, our results demonstrate that MLL-ELL requires the presence of intact ELL(eCT) in order to disrupt p53 interactions with p300/CBP coactivator and thus significantly reduce p53 acetylation in vivo. Since ELL(eCT) has recently been shown to be both necessary and sufficient for MLL-ELL-mediated transformation of normal blood progenitors, our data correlate ELL(eCT) contribution to MLL-ELL transformative effects with its ability to functionally inhibit p53.

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Changes in splicing and neuromodulatory gene expression programs in sensory neurons with pheromone signaling and social experience

10.1101/2021.06.18.449021 ◽

2021 ◽

Author(s):

Pelin C Volkan ◽

Bryson Deanhardt ◽

Qichen Duan ◽

Chengcheng Du ◽

Charles Soeder ◽

...

Keyword(s):

Sensory Neurons ◽

Molecular Mechanisms ◽

Social Experience ◽

Rna Seq ◽

Male Courtship ◽

Wild Type ◽

Pheromone Signaling ◽

Courtship Behaviors ◽

Necessary And Sufficient ◽

Splicing Patterns

Social experience and pheromone signaling in ORNs affect pheromone responses and male courtship behaviors in Drosophila, however, the molecular mechanisms underlying this circuit-level neuromodulation remain less clear. Previous studies identified social experience and pheromone signaling-dependent modulation of chromatin around behavioral switch gene fruitless, which encodes a transcription factor necessary and sufficient for male behaviors. To identify the molecular mechanisms driving social experience-dependent neuromodulation, we performed RNA-seq from antennal samples of mutant fruit flies in pheromone receptors and fruitless, as well as grouped or isolated wild-type males. We found that loss of pheromone detection differentially alters the levels of fruitless exons suggesting changes in splicing patterns. In addition, many Fruitless target neuromodulatory genes, such as neurotransmitter receptors, ion channels, and ion transporters, are differentially regulated by social context and pheromone signaling. Our results suggest that modulation of circuit activity and behaviors in response to social experience and pheromone signaling arise due to changes in transcriptional programs for neuromodulators downstream of behavioral switch gene function.

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Proteomic analysis demonstrated transcription factor YRR1 gene deletion in Saccharomyces cerevisiae enhances its resistance to vanillin through the upregulation of transcriptional activator Haa1, coactivator Mbf1, and proteasome assembly chaperone Tma17 expression

10.21203/rs.2.24803/v1 ◽

2020 ◽

Author(s):

Wenyan Cao ◽

Xinning Wang ◽

Weiquan Zhao ◽

Yu Shen ◽

Wensheng Qin ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Transcription Factor ◽

Ribosomal Proteins ◽

Molecular Mechanisms ◽

Transcriptional Activator ◽

Wild Type ◽

Translation Process ◽

Enhanced Resistance ◽

Yeast Strains ◽

Transcriptomic Changes

Abstract Background: Vanillin is one of the major phenolic inhibitors in Saccharomyces cerevisiae for cellulosic ethanol production. Deleting transcription factor gene YRR1 improves vanillin resistance by promoting some translation-related processes that were confirmed at the transcription level in our previous studies. However, the known genes regulated by Yrr1 are not related to translation process. Therefore, in this work, we investigated the effects of proteomic changes on vanillin stress and YRR1 deletion to provide different perspectives from transcriptome analysis for comprehending the mechanisms of YRR1 deletion in yeast protective response to vanillin.Results: In wild-type cells, vanillin reduced the numbers of ribosomal proteins quantities and thereby inhibited cells’ translation. YRR1 deletion changed the quantities of 121 proteins which have no overlaps with transcriptomic changes. Of 112 proteins were up-regulated; 48 of 112 up-regulated proteins are involved in stress response, translational and basal transcriptional regulation. Fermentation data showed that the overexpression of HAA1, MBF1, and TMA17, which encode transcriptional activator, coactivator, and proteasome assembly chaperone, respectively, enhanced resistance to vanillin in S. cerevisiae. Conclusions: These results showed how YRR1 deletion increase vanillin resistance at protein level. This may advance our understanding of molecular mechanisms for YRR1 deletion to protect yeast from vanillin stress and offer novel targets of genetic engineering for designing inhibitor-resistant ethanologenic yeast strains.

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Constitutive Expression of a Nag-Like Dioxygenase Gene through an Internal Promoter in the 2-Chloronitrobenzene Catabolism Gene Cluster of Pseudomonas stutzeri ZWLR2-1

Applied and Environmental Microbiology ◽

10.1128/aem.00197-16 ◽

2016 ◽

Vol 82 (12) ◽

pp. 3461-3470 ◽

Cited By ~ 9

Author(s):

Yi-Zhou Gao ◽

Hong Liu ◽

Hong-Jun Chao ◽

Ning-Yi Zhou

Keyword(s):

Gene Cluster ◽

Molecular Mechanisms ◽

Expression System ◽

Constitutive Expression ◽

Pseudomonas Stutzeri ◽

Initial Reaction ◽

Synthetic Compounds ◽

Content Type ◽

Dioxygenase Gene ◽

Catabolism Pathway

ABSTRACTThe gene cluster encoding the 2-chloronitrobenzene (2CNB) catabolism pathway inPseudomonas stutzeriZWLR2-1 is a patchwork assembly of a Nag-like dioxygenase (dioxygenase belonging to the naphthalene dioxygenase NagAaAbAcAd family fromRalstoniasp. strain U2) gene cluster and a chlorocatechol catabolism cluster. However, the transcriptional regulator gene usually present in the Nag-like dioxygenase gene cluster is missing, leaving it unclear how this cluster is expressed. The pattern of expression of the 2CNB catabolism cluster was investigated here. The results demonstrate that the expression was constitutive and not induced by its substrate 2CNB or salicylate, the usual inducer of expression in the Nag-like dioxygenase family. Reverse transcription-PCR indicated the presence of at least one transcript containing all the structural genes for 2CNB degradation. Among the three promoters verified in the gene cluster, P1 served as the promoter for the entire catabolism operon, but the internal promoters P2 and P3 also enhanced the transcription of the genes downstream. The P3 promoter, which was not previously defined as a promoter sequence, was the strongest of these three promoters. It drove the expression ofcnbAcAdencoding the dioxygenase that catalyzes the initial reaction in the 2CNB catabolism pathway. Bioinformatics and mutation analyses suggested that this P3 promoter evolved through the duplication of an 18-bp fragment and introduction of an extra 132-bp fragment.IMPORTANCEThe release of many synthetic compounds into the environment places selective pressure on bacteria to develop their ability to utilize these chemicals to grow. One of the problems that a bacterium must surmount is to evolve a regulatory device for expression of the corresponding catabolism genes. Considering that 2CNB is a xenobiotic that has existed only since the onset of synthetic chemistry, it may be a good example for studying the molecular mechanisms underlying rapid evolution in regulatory networks for the catabolism of synthetic compounds. The 2CNB utilizerPseudomonas stutzeriZWLR2-1 in this study has adapted itself to the new pollutant by evolving the always-inducible Nag-like dioxygenase into a constitutively expressed enzyme, and its expression has escaped the influence of salicylate. This may facilitate an understanding of how bacteria can rapidly adapt to the new synthetic compounds by evolving its expression system for key enzymes involved in the degradation of a xenobiotic.

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Structure and Regulation of the gab Gene Cluster, Involved in the γ-Aminobutyric Acid Shunt, Are Controlled by a σ54 Factor in Bacillus thuringiensis

Journal of Bacteriology ◽

10.1128/jb.01038-09 ◽

2009 ◽

Vol 192 (1) ◽

pp. 346-355 ◽

Cited By ~ 19

Author(s):

Li Zhu ◽

Qi Peng ◽

Fuping Song ◽

Yanan Jiang ◽

Changpo Sun ◽

...

Keyword(s):

Bacillus Thuringiensis ◽

Gene Cluster ◽

Culture Media ◽

Consensus Sequence ◽

Aminobutyric Acid ◽

Transcription Activator ◽

Gaba Shunt ◽

Reverse Transcription Pcr ◽

Transcriptional Units ◽

Fusion Analysis

ABSTRACT The structure and regulation of the gab gene cluster, involved in γ-aminobutyric acid (GABA) shunt, were studied by characterizing gabT and gabD genes cloned from Bacillus thuringiensis. Deletions of the gabT and gabD genes in B. thuringiensis strain HD-73 did not affect the growth of mutant strains in rich culture media, but the growth of a gabT deletion mutant strain was reduced in basic media (containing 0.2% GABA). Genome analysis indicates that the structure of the gab gene cluster in B. thuringiensis HD-73 is different from that in Escherichia coli and Bacillus subtilis but is common in strains of the Bacillus cereus group. This suggests that the gene cluster involved in GABA shunt is specific to the B. cereus group. Based on reverse transcription-PCR and transcriptional fusion analysis, we confirmed that the gabT and gabD genes belong to different transcriptional units, while the gabD and gabR genes form an operon. We also demonstrated that the gabR gene plays a positive regulatory role in gabD and gabT expression. The GabR protein may be a σ54-dependent transcriptional activator, according to a conserved domain search in the NCBI database, and it is highly conserved in the B. cereus group. The −24/−12 consensus sequence of a promoter upstream from gabT suggests that the promoter can be recognized by a σ54 factor. Further analysis of the genetic complementation studies also suggests that the expression of the gabT gene is controlled by a σ54 factor. Thus, the expression of the gab cluster is regulated by a σ54 factor by way of the transcription activator GabR.

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QscR, a LysR-Type Transcriptional Regulator and CbbR Homolog, Is Involved in Regulation of the Serine Cycle Genes in Methylobacterium extorquens AM1

Journal of Bacteriology ◽

10.1128/jb.185.4.1229-1235.2003 ◽

2003 ◽

Vol 185 (4) ◽

pp. 1229-1235 ◽

Cited By ~ 23

Author(s):

Marina G. Kalyuzhnaya ◽

Mary E. Lidstrom

Keyword(s):

Specific Binding ◽

Transcriptional Regulator ◽

Wild Type ◽

Methylobacterium Extorquens ◽

Reverse Transcription Pcr ◽

Promoter Fusion ◽

Key Enzyme ◽

New Gene ◽

Transcriptional Units ◽

Glyoxylate Aminotransferase

ABSTRACT A new gene, qscR, encoding a LysR-type transcriptional regulator that is a homolog of CbbR, has been characterized from the facultative methylotroph Methylobacterium extorquens AM1 and shown to be the major regulator of the serine cycle, the specific C1 assimilation pathway. The qscR mutant was shown to be unable to grow on C1 compounds, and it lacked the activity of serine-glyoxylate aminotransferase, a key enzyme of the serine cycle. Activities of other serine cycle enzymes were decreased during growth on C1 compounds compared to the activities found in wild-type M. extorquens AM1. Promoter fusion assays, as well as reverse transcription-PCR assays, have indicated that the serine cycle genes belong to three separate transcriptional units, sga-hpr-mtdA-fch, mtkA-mtkB-ppc-mcl, and gly. Gel retardation assays involving the purified QscR have demonstrated the specific binding of QscR to the DNA regions upstream of sga, mtkA, gly, and qscR. We conclude that QscR acts as a positive transcriptional regulator of most of the serine cycle enzymes and also as an autorepressor.

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