scholarly journals Involvement of the Cra Global Regulatory Protein in the Expression of the iscRSUA Operon, Revealed during Studies of Tricarballylate Catabolism in Salmonella enterica

2009 ◽  
Vol 191 (7) ◽  
pp. 2069-2076 ◽  
Author(s):  
Jeffrey A. Lewis ◽  
Jeffrey M. Boyd ◽  
Diana M. Downs ◽  
Jorge C. Escalante-Semerena
Keyword(s):  
Binding Sites ◽  
Salmonella Enterica ◽  
Promoter Region ◽  
Flavin Adenine Dinucleotide ◽  
Regulatory Protein ◽  
Regulatory Region ◽  
Cluster Assembly ◽  
Regulation Of Expression ◽  
Membrane Bound ◽  
Low Levels

ABSTRACT In Salmonella enterica, tricarballylate (Tcb) catabolism requires function of TcuB, a membrane-bound protein that contains [4Fe-4S] clusters and heme. TcuB transfers electrons from reduced flavin adenine dinucleotide in the Tcb dehydrogenase (TcuA) to electron acceptors in the membrane. We recently showed that functions needed to assemble [Fe-S] clusters (i.e., the iscRSUA-hscBA-fdx operon) compensate for the lack of ApbC during growth of an apbC strain on Tcb. ApbC had been linked to [Fe-S] cluster metabolism, and we showed that an apbC strain had decreased TcuB activity. Here we report findings that expand our understanding of the regulation of expression of the iscRSUA genes in Salmonella enterica. We investigated why low levels of glucose or other saccharides restored growth of an apbC strain on Tcb. Here we report the following findings. (i) A ≤1 mM concentration of glucose, fructose, ribose, or glycerol restores growth of an apbC strain on Tcb. (ii) The saccharide effect results in increased levels of TcuB activity. (iii) The saccharide effect depends on the global regulatory protein Cra. (iv) Putative Cra binding sites are present in the regulatory region of the iscRSUA operon. (v) Cra protein binds to all three sites in the iscRSUA promoter region in a concentration-dependent fashion. To our knowledge, this is the first report of the involvement of Cra in [Fe-S] cluster assembly.

scholarly journals Bioinformatics Analysis of SNPs in IL-6 Gene Promoter of Jinghai Yellow Chickens

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 446 ◽  
Author(s):  
Shijie Xin ◽  
Xiaohui Wang ◽  
Guojun Dai ◽  
Jingjing Zhang ◽  
Tingting An ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Binding Sites ◽  
Promoter Region ◽  
Bioinformatics Analysis ◽  
Cpg Islands ◽  
Regulatory Region ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Factor Binding

The proinflammatory cytokine, interleukin-6 (IL-6), plays a critical role in many chronic inflammatory diseases, particularly inflammatory bowel disease. To investigate the regulation of IL-6 gene expression at the molecular level, genomic DNA sequencing of Jinghai yellow chickens (Gallus gallus) was performed to detect single-nucleotide polymorphisms (SNPs) in the region −2200 base pairs (bp) upstream to 500 bp downstream of IL-6. Transcription factor binding sites and CpG islands in the IL-6 promoter region were predicted using bioinformatics software. Twenty-eight SNP sites were identified in IL-6. Four of these 28 SNPs, three [−357 (G > A), −447 (C > G), and −663 (A > G)] in the 5′ regulatory region and one in the 3′ non-coding region [3177 (C > T)] are not labelled in GenBank. Bioinformatics analysis revealed 11 SNPs within the promoter region that altered putative transcription factor binding sites. Furthermore, the C-939G mutation in the promoter region may change the number of CpG islands, and SNPs in the 5′ regulatory region may influence IL-6 gene expression by altering transcription factor binding or CpG methylation status. Genetic diversity analysis revealed that the newly discovered A-663G site significantly deviated from Hardy-Weinberg equilibrium. These results provide a basis for further exploration of the promoter function of the IL-6 gene and the relationships of these SNPs to intestinal inflammation resistance in chickens.

scholarly journals Regulation of Expression of the 2-Deoxy-d-Ribose Utilization Regulon, deoQKPX, from Salmonella enterica Serovar Typhimurium

2003 ◽  
Vol 185 (20) ◽  
pp. 6042-6050 ◽  
Author(s):  
Mette Christensen ◽  
Tudor Borza ◽  
Gert Dandanell ◽  
Anne-Marie Gilles ◽  
Octavian Barzu ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Transcription Initiation ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Regulatory Protein ◽  
Genetic Determinants ◽  
Promoter Regions ◽  
Regulation Of Expression ◽  
Serovar Typhimurium ◽  
In Silico Analyses ◽  
Extension Analysis

ABSTRACT Salmonella enterica, in contrast to Escherichia coli K12, can use 2-deoxy-d-ribose as the sole carbon source. The genetic determinants for this capacity in S. enterica serovar Typhimurium include four genes, of which three, deoK, deoP, and deoX, constitute an operon. The fourth, deoQ, is transcribed in the opposite direction. The deoK gene encodes deoxyribokinase. In silico analyses indicated that deoP encodes a permease and deoQ encodes a regulatory protein of the deoR family. The deoX gene product showed no match to known proteins in the databases. Deletion analyses showed that both a functional deoP gene and a functional deoX gene were required for optimal utilization of deoxyribose. Using gene fusion technology, we observed that deoQ and the deoKPX operon were transcribed from divergent promoters located in the 324-bp intercistronic region between deoQ and deoK. The deoKPX promoter was 10-fold stronger than the deoQ promoter, and expression was negatively regulated by DeoQ as well as by DeoR, the repressor of the deoxynucleoside catabolism operon. Transcription of deoKPX but not of deoQ was regulated by catabolite repression. Primer extension analysis identified the transcriptional start points of both promoters and showed that induction by deoxyribose occurred at the level of transcription initiation. Gel retardation experiments with purified DeoQ illustrated that it binds independently to tandem operator sites within the deoQ and deoK promoter regions with Kd values of 54 and 2.4 nM, respectively.

scholarly journals New Polymorphisms in Regulatory Region of CAPN3 Gene with no Effect on Gene Expression in Breast Muscle of Broiler Chickens

2014 ◽  
Vol 14 (3) ◽  
pp. 511-524 ◽  
Author(s):  
Katarzyna Piórkowska ◽  
Joanna Nowak ◽  
Katarzyna Połtowicz ◽  
Katarzyna Ropka-Molik
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Promoter Region ◽  
Broiler Chickens ◽  
Regulatory Region ◽  
Restriction Enzymes ◽  
Transcript Abundance ◽  
Cysteine Proteases ◽  
Cell Growth And Migration ◽  
Capn3 Gene

AbstractCalpains are enzymes that belong to calcium-dependent, non-lysosomal cysteine proteases. The CAPN3 gene encodes a major intracellular specific muscle protease with a high capacity for degradation of cytoskeletal and muscle fibre proteins. Therefore, they play an important role in fusion of myoblasts, proliferation, cell growth and migration. In chickens, the gene encoding for calpain 3 is localized on chromosome 5. Due to the function of encoded protein, the CAPN3 has beenchosen as a candidate gene for meat quality in chickens. Consequently, the aim of our study was to identify new polymorphisms in the regulatory region of CAPN3 gene and to investigate their impact on CAPN3 transcript abundance in breast muscles. The experiment used broilers of two genetic lines: fast- and slow-growing. The polymorphisms were identified by screening with High Resolution Melting (HRM) and sequencing based on the Sanger method. The CAPN3 gene expression was conducted by using succinate dehydrogenase complex, subunit A (SDHA) and 60S ribosomal protein L4 (RPL4) genes as endogenous controls. Four new polymorphisms were found: g.322176G>A in promoter region (GenBank: AADN03004661.1), c.176*C>T, c.144*G>C and c.137*_147*delCAGCCCTGCTT in 3`UTR sequence. The new polymorphisms were identified by using restriction enzymes ScrFI, BslI, AcuI, HpyAV, respectively. The frequency of polymorphisms found in 3`UTR region was similar in both lines. According to polymorphisms identified in 3`UTR region the alleles with deletion, C and C (c.137*_147*del, c.144*G>C and c.176*C>T) were rare. The polymorphism identified in the promoter region and 3`UTR regions changed a few binding sites for transcription factors, but did not alter any binding sites for the other important translation regulators such as miRNA. Analysis of the effect of new polymorphisms on CAPN3 gene expression showed that in fast-growing line the chickens with GG genotype according to polymorphism g.322176G>A inthe promoter region, were characterized by the highest CAPN3 transcript abundance. Other polymorphisms in 3>UTR region seem to have no effect on CAPN3 gene expression.

scholarly journals HIF 1 inhibits STAR transcription and testosterone synthesis in murine Leydig cells

2019 ◽  
Vol 62 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Xueting Wang ◽  
Zhiran Zou ◽  
Zhihui Yang ◽  
Shan Jiang ◽  
Yapeng Lu ◽  
...  
Keyword(s):  
Testosterone Level ◽  
Binding Sites ◽  
Promoter Region ◽  
Leydig Cells ◽  
Regulatory Protein ◽  
Hydroxysteroid Dehydrogenase ◽  
Luciferase Reporter ◽  
Steroid Synthesis ◽  
Software Analysis ◽  
Testosterone Synthesis

Hypoxia-inducible factor-1 (HIF1) is a critical transcription factor involved in cell response to hypoxia. Under physiological conditions, its ‘a’ subunit is rapidly degraded in most tissues except testes. HIF1 is stably expressed in Leydig cells, which are the main source of testosterone for male, and might bind to the promoter region of steroidogenic acute regulatory protein (STAR), which is necessary for the testosterone synthesis, according to software analysis. This study aims to identify the binding sites of HIF1 onStarpromoter and its transcriptional regulation of STAR to affect testosterone synthesis. Testosterone level and steroid synthesis-related proteins were determined in male Balb/C mice exposed to hypoxia (8% O2). While HIF1 was upregulated, the testosterone level was significantly decreased. This was further confirmed byin vitroexperiments with rat primary Leydig cells or TM3 cells exposed to hypoxia (1% O2), CoCl2or DFX to raise HIF1. The decline of testosterone was reversed by pregnenolone but not cAMP, indicating the cholesterol transport disorder as the main cause. In agreement, STAR expression level was decreased in response to HIF1, while 3b-hydroxysteroid dehydrogenase, 17b-hydroxysteroid dehydrogenase and p450scc did not exhibit significant changes. By ChIP, EMSA supershift and dual-luciferase reporter assays, HIF1 was found to bind to theStarpromoter region and repress the expression of STAR. Mutation assays identified three HIF1-binding sites on mouseStarpromoter. These findings indicate that HIF1 represses STAR transcription through directly binding to theStaarpromoter at −2082/−2078, −2064/−2060 and −1910/−1906, leading to the negative regulation of testosterone synthesis.

scholarly journals The Leucine-Responsive Regulatory Protein, Lrp, Activates Transcription of the fim Operon in Salmonella enterica Serovar Typhimurium via the fimZ Regulatory Gene

2007 ◽  
Vol 190 (2) ◽  
pp. 602-612 ◽  
Author(s):  
Kirsty A. McFarland ◽  
Sacha Lucchini ◽  
Jay C. D. Hinton ◽  
Charles J. Dorman
Keyword(s):  
Gene Expression ◽  
Salmonella Enterica ◽  
Regulatory Protein ◽  
Regulatory Region ◽  
Upstream Region ◽  
Positive Contribution ◽  
Type 1 Fimbriae ◽  
Regulatory Cascade ◽  
Serovar Typhimurium

ABSTRACT The fim operon of Salmonella enterica serovar Typhimurium encodes type 1 fimbriae. The expression of fim is controlled in response to environmental signals through a complex regulatory cascade involving the proteins FimW, FimY, and FimZ and a genetic locus, fimU, that encodes a rare arginine tRNA. We discovered that a knockout mutation in lrp, the gene that codes for the leucine-responsive regulatory protein (Lrp), inhibited fim transcription. The loss of fim gene expression was accompanied by a corresponding loss of the mannose-sensitive hemagglutination that is a characteristic of type 1 fimbriae. Normal type 1 fimbrial expression was restored following the introduction into the knockout mutant of a plasmid carrying a functional copy of the lrp gene. Electrophoretic mobility shift analysis revealed no interactions between purified Lrp protein and the regulatory region of the fimA, fimU, or fimW gene. Instead, Lrp produced protein-DNA complexes with the regulatory region of the fimZ gene, and the nature of these complexes was leucine sensitive. DNase I footprinting showed that Lrp binds within a region between −65 and −170 with respect to the fimZ transcription start site, consistent with the binding and wrapping of the DNA in this upstream region. Ectopic expression of the fimZ gene from an inducible promoter caused Lrp-independent type 1 fimbriation in serovar Typhimurium. These data show that Lrp makes a positive contribution to fim gene expression through direct interaction with the fimZ promoter region, possibly by antagonizing the binding of the H-NS global repressor protein.

scholarly journals Molecular Cloning and Transcriptional Regulation of the Aspergillus nidulans xlnD Gene Encoding a β-Xylosidase

1998 ◽  
Vol 64 (4) ◽  
pp. 1412-1419 ◽  
Author(s):  
José A. Pérez-González ◽  
Noël N. M. E. van Peij ◽  
Alja Bezoen ◽  
Andrew P. Maccabe ◽  
Daniel Ramón ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Aspergillus Nidulans ◽  
Binding Sites ◽  
Glucose Repression ◽  
Regulatory Protein ◽  
Regulatory Region ◽  
Northern Analysis ◽  
Transcriptional Level ◽  
Gene Encoding ◽  
Primary Structures

ABSTRACT The xlnD gene encoding the 85-kDa β-xylosidase was cloned from Aspergillus nidulans. The deduced primary structure of the protein exhibits considerable similarity to the primary structures of the Aspergillus niger andTrichoderma reesei β-xylosidases and some similarity to the primary structures of the class 3 β-glucosidases.xlnD is regulated at the transcriptional level; it is induced by xylan and d-xylose and is repressed byd-glucose. Glucose repression is mediated by the product of the creA gene. Although several binding sites for the pH regulatory protein PacC were found in the upstream regulatory region, it was not clear from a Northern analysis whether PacC is involved in transcriptional regulation of xlnD.

scholarly journals Temperature- and H-NS-Dependent Regulation of a Plasmid-Encoded Virulence Operon Expressing Escherichia coli Hemolysin

2002 ◽  
Vol 184 (18) ◽  
pp. 5058-5066 ◽  
Author(s):  
Cristina Madrid ◽  
José M. Nieto ◽  
Sònia Paytubi ◽  
Maurizio Falconi ◽  
Claudio O. Gualerzi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Binding Sites ◽  
Promoter Region ◽  
Regulatory Region ◽  
Upstream Site ◽  
Nucleoprotein Complex ◽  
Dna Fragment ◽  
Escherichia Coli Hemolysin ◽  
Specific Sequences

ABSTRACT Proteins H-NS and Hha form a nucleoprotein complex that modulates expression of the thermoregulated hly operon of Escherichia coli. We have been able to identify two H-NS binding sites in the hly regulatory region. One of them partially overlaps the promoter region (site II), and the other is located about 2 kbp upstream (site I). In contrast, Hha protein did not show any preference for specific sequences. In vitro, temperature influences the affinity of H-NS for a DNA fragment containing both binding sites and H-NS-mediated repression of hly operon transcription. Deletion analysis of the hly regulatory region confirms the relevance of site I for thermoregulation of this operon. We present a model to explain the temperature-modulated repression of the hly operon, based on the experiments reported here and other, preexisting data.

The expression ofnifBgene fromHerbaspirillum seropedicaeis dependent upon the NifA and RpoN proteins

2006 ◽  
Vol 52 (12) ◽  
pp. 1199-1207 ◽  
Author(s):  
Fabiane G.M Rego ◽  
Fábio O Pedrosa ◽  
Leda S Chubatsu ◽  
M Geoffrey Yates ◽  
Roseli Wassem ◽  
...  
Keyword(s):  
Binding Sites ◽  
Promoter Region ◽  
Integration Host Factor ◽  
Lacz Fusion ◽  
Herbaspirillum Seropedicae ◽  
Band Shift ◽  
E Coli ◽  
Low Levels ◽  
Ihf Protein

The putative nifB promoter region of Herbaspirillum seropedicae contained two sequences homologous to NifA-binding site and a –24/–12 type promoter. A nifB::lacZ fusion was assayed in the backgrounds of both Escherichia coli and H. seropedicae. In E. coli, the expression of nifB::lacZ occurred only in the presence of functional rpoN and Klebsiella pneumoniae nifA genes. In addition, the integration host factor (IHF) stimulated the expression of the nifB::lacZ fusion in this background. In H. seropedicae, nifB expression occurred only in the absence of ammonium and under low levels of oxygen, and it was shown to be strictly dependent on NifA. DNA band shift experiments showed that purified K. pneumoniae RpoN and E. coli IHF proteins were capable of binding to the nifB promoter region, and in vivo dimethylsulfate footprinting showed that NifA binds to both NifA-binding sites. These results strongly suggest that the expression of the nifB promoter of H. seropedicae is dependent on the NifA and RpoN proteins and that the IHF protein stimulates NifA activation of nifB promoter.Key words: Herbaspirillum seropedicae, nif, nitrogen fixation, NifA, RpoN.

scholarly journals Induction of the Cellular E2F-1 Promoter by the Adenovirus E4-6/7 Protein

2000 ◽  
Vol 74 (5) ◽  
pp. 2084-2093 ◽  
Author(s):  
Joel Schaley ◽  
Robert J. O'Connor ◽  
Laura J. Taylor ◽  
Dafna Bar-Sagi ◽  
Patrick Hearing
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Transient Expression ◽  
Binding Sites ◽  
Promoter Region ◽  
Fluorescent Protein ◽  
Protein Accumulation ◽  
Promoter Regions ◽  
Single Binding Site

ABSTRACT The adenovirus type 5 (Ad5) E4-6/7 protein interacts directly with different members of the E2F family and mediates the cooperative and stable binding of E2F to a unique pair of binding sites in the Ad5 E2a promoter region. This induction of E2F DNA binding activity strongly correlates with increased E2a transcription when analyzed using virus infection and transient expression assays. Here we show that while different adenovirus isolates express an E4-6/7 protein that is capable of induction of E2F dimerization and stable DNA binding to the Ad5 E2a promoter region, not all of these viruses carry the inverted E2F binding site targets in their E2a promoter regions. The Ad12 and Ad40 E2a promoter regions bind E2F via a single binding site. However, these promoters bind adenovirus-induced (dimerized) E2F very weakly. The Ad3 E2a promoter region binds E2F very poorly, even via a single binding site. A possible explanation of these results is that the Ad E4-6/7 protein evolved to induce cellular gene expression. Consistent with this notion, we show that infection with different adenovirus isolates induces the binding of E2F to an inverted configuration of binding sites present in the cellular E2F-1 promoter. Transient expression of the E4-6/7 protein alone in uninfected cells is sufficient to induce transactivation of the E2F-1 promoter linked to chloramphenicol acetyltransferase or green fluorescent protein reporter genes. Further, expression of the E4-6/7 protein in the context of adenovirus infection induces E2F-1 protein accumulation. Thus, the induction of E2F binding to the E2F-1 promoter by the E4-6/7 protein observed in vitro correlates with transactivation of E2F-1 promoter activity in vivo. These results suggest that adenovirus has evolved two distinct mechanisms to induce the expression of the E2F-1 gene. The E1A proteins displace repressors of E2F activity (the Rb family members) and thus relieve E2F-1 promoter repression; the E4-6/7 protein complements this function by stably recruiting active E2F to the E2F-1 promoter to transactivate expression.

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