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Transcription Regulators (transcription + regulator)
Selected AbstractsThe cell migration protein Grb7 associates with transcriptional regulator FHL2 in a Grb7 phosphorylation-dependent mannerJOURNAL OF MOLECULAR RECOGNITION, Issue 1 2009Sharareh Siamakpour-Reihani Abstract Grb7 is an adaptor molecule that can mediate signal transduction from multiple cell surface receptors to various downstream signaling pathways. Grb7, along with Grb10 and Grb14, make up the Grb7 protein family. This protein family has been shown to be overexpressed in certain cancers and cancer cell lines. Grb7 and a receptor tyrosine kinase (RTK), erbB2, are overexpressed in 20,30% of breast cancers. Grb7 overexpression has been linked to enhanced cell migration and metastasis, though the participants in these pathways have not been determined. In this study, we report that Grb7 interacts with four and half lim domains isoform 2 (FHL2), a transcription regulator with an important role in oncogenesis, including breast cancer. Additionally, in yeast 2-hybrid (Y2H) assays, we show that the interaction is specific to the Grb7 RA and PH domains. We have also demonstrated that full-length (FL) Grb7 and FHL2 interact in mammalian cells and that Grb7 must be tyrosine phosphorylated for this interaction to occur. Immunofluorescent microscopy demonstrates possible co-localization of Grb7 and FHL2. A model with supporting NMR evidence of Grb7 autoinhibition is proposed. Copyright © 2008 John Wiley & Sons, Ltd. [source] Characterization of CidR-mediated regulation in Bacillus anthracis reveals a previously undetected role of S-layer proteins as murein hydrolasesMOLECULAR MICROBIOLOGY, Issue 4 2006Jong-Sam Ahn Summary Recent studies have shown that the Staphylococcus aureus cidABC and lrgAB operons are involved in the regulation of cell death and lysis. The transcription of cidABC and lrgAB was shown to be induced by acetic acid and was dependent on the cidR gene encoding a new member of the LysR-type transcription regulator (LTTR) family of proteins. In the study presented here, we examined the phenotypic and regulatory effects of disrupting a cidR homologue in Bacillus anthracis. As in S. aureus, the cidR mutation affected expression of the B. anthracis cid and lrg homologues, murein hydrolase activity and cell viability in stationary phase. Interestingly, the predominant murein hydrolase affected was an 85 kDa protein that was identified as Sap, a primary constituent of the S-layer in B. anthracis. The ability of Sap, as well as its counterpart EA1, to exhibit murein hydrolase activity was confirmed by cloning their respective genes in Escherichia coli and showing that the overexpressed proteins contained this activity. Northern blot analyses revealed that the cidR mutation caused reduced transcription of the genes encoding Sap and EA1, as well as CsaB involved in the attachment of the S-layer proteins to the cell wall. The results of these studies not only establish the existence of the cid and lrg murein hydrolase regulatory network in B. anthracis, but also help to define the function and regulation of the S-layer proteins. [source] A Study of the Interaction between Auxin and Ethylene in Wild Type and Transgenic Ethylene-Insensitive Tobacco during Adventitious Root Formation Induced by Stagnant Root Zone ConditionsPLANT BIOLOGY, Issue 5 2003M. P. McDonald Abstract: Wild type (Wt) and transgenic plants (etr1-1 gene from Arabidopsis thaliana; encoding for a defective ethylene receptor; Tetr) of Nicotiana tabacum L. were subjected to experiments to resolve the role of the interaction between ethylene and auxin in waterlogging-induced adventitious root formation. Plants were grown in aerated or stagnant deoxygenated nutrient solution and treated with the following plant growth regulators: ethylene, the synthetic auxins 2,4-dichlorophenoxyacetic acid (2,4-D) and 1-naphthaleneacetic acid (1-NAA), and the auxin efflux inhibitor naphthylphthalamic acid (NPA). The superior growth of Wt in stagnant solution suggests that the ability to sense and respond to ethylene partially mediates tolerance to stagnant root zone conditions. Wt produced around 2 - 2.5-fold more adventitious roots than Tetr in aerated and stagnant solution. Treatment with NPA phenocopied the effects of ethylene insensitivity by reducing the number of adventitious roots on Wt to Tetr levels. Additionally, application of 1-NAA to the shoot of Tetr increased the number of adventitious roots on Tetr to similar levels as the untreated Wt. However, this level was only around half the number achieved by 1-NAA-treated Wt. The results suggest an interplay between ethylene and auxin in the process of adventitious root formation in waterlogged tobacco, most likely on the level of polar auxin transport. However, a separate non-auxin-related role as a transcription regulator for genes essential to adventitious root formation cannot be excluded. [source] Variants within MECP2, a key transcription regulator, are associated with increased susceptibility to lupus and differential gene expression in patients with systemic lupus erythematosusARTHRITIS & RHEUMATISM, Issue 4 2009Ryan Webb Objective Both genetic and epigenetic factors play an important role in the pathogenesis of lupus. The aim of this study was to examine methyl-CpG,binding protein 2 gene (MECP2) polymorphisms in a large cohort of patients with lupus and control subjects, and to determine the functional consequences of the lupus-associated MECP2 haplotype. Methods We genotyped 18 single-nucleotide polymorphisms within MECP2, located on chromosome Xq28, in a large cohort of patients with lupus and control subjects of European descent. We studied the functional effects of the lupus-associated MECP2 haplotype by determining gene expression profiles in B cell lines in female lupus patients with and those without the lupus-associated MECP2 risk haplotype. Results We confirmed, replicated, and extended the genetic association between lupus and genetic markers within MECP2 in a large independent cohort of lupus patients and control subjects of European descent (odds ratio 1.35, P = 6.65 × 10,11). MECP2 is a dichotomous transcription regulator that either activates or represses gene expression. We identified 128 genes that are differentially expressed in lupus patients with the disease-associated MECP2 haplotype; most (,81%) were up-regulated. Genes that were up-regulated had significantly more CpG islands in their promoter regions compared with genes that were down-regulated. Gene ontology analysis using the differentially expressed genes revealed significant association with epigenetic regulatory mechanisms, suggesting that these genes are targets for MECP2 regulation in B cells. Furthermore, at least 13 of the 104 up-regulated genes are regulated by interferon. The disease-risk MECP2 haplotype was associated with increased expression of the MECP2 transcription coactivator CREB1 and decreased expression of the corepressor histone deacetylase 1. Conclusion Polymorphism in the MECP2 locus is associated with lupus and, at least in part, contributes to the interferon signature observed in lupus patients. [source] Metabolic engineering of Escherichia coli for the production of putrescine: A four carbon diamineBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2009Zhi-Gang Qian Abstract A four carbon linear chain diamine, putrescine (1,4-diaminobutane), is an important platform chemical having a wide range of applications in chemical industry. Biotechnological production of putrescine from renewable feedstock is a promising alternative to the chemical synthesis that originates from non-renewable petroleum. Here we report development of a metabolically engineered strain of Escherichia coli that produces putrescine at high titer in glucose mineral salts medium. First, a base strain was constructed by inactivating the putrescine degradation and utilization pathways, and deleting the ornithine carbamoyltransferase chain I gene argI to make more precursors available for putrescine synthesis. Next, ornithine decarboxylase, which converts ornithine to putrescine, was amplified by a combination of plasmid-based and chromosome-based overexpression of the coding genes under the strong tac or trc promoter. Furthermore, the ornithine biosynthetic genes (argC-E) were overexpressed from the trc promoter, which replaced the native promoter in the genome, to increase the ornithine pool. Finally, strain performance was further improved by the deletion of the stress responsive RNA polymerase sigma factor RpoS, a well-known global transcription regulator that controls the expression of ca. 10% of the E. coli genes. The final engineered E. coli strain was able to produce 1.68,g,L,1 of putrescine with a yield of 0.168,g,g,1 glucose. Furthermore, high cell density cultivation allowed production of 24.2,g,L,1 of putrescine with a productivity of 0.75,g,L,1,h,1. The strategy reported here should be useful for the bio-based production of putrescine from renewable resources, and also for the development of strains capable of producing other diamines, which are important as nitrogen-containing platform chemicals. Biotechnol. Bioeng. 2009; 104: 651,662 © 2009 Wiley Periodicals, Inc. [source] Differential effects of acute and chronic exercise on plasticity-related genes in the rat hippocampus revealed by microarrayEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 6 2002Raffaella Molteni Abstract Studies were performed to determine the effects of acute and chronic voluntary periods of exercise on the expression of hippocampal genes. RNAs from rodents exposed to a running wheel for 3, 7 and 28 days were examined using a microarray with 1176 cDNAs expressed primarily in the brain. The expression of selected genes was quantified by Taqman RT-PCR or RNase protection assay. The largest up-regulation was observed in genes involved with synaptic trafficking (synapsin I, synaptotagmin and syntaxin); signal transduction pathways (Ca2+/calmodulin-dependent protein kinase II, CaM-KII; mitogen-activated/extracellular signal-regulated protein kinase, MAP-K/ERK I and II; protein kinase C, PKC-,) or transcription regulators (cyclic AMP response element binding protein, CREB). Genes associated with the glutamatergic system were up-regulated (N -methyl- d -aspartate receptor, NMDAR-2A and NMDAR-2B and excitatory amino acid carrier 1, EAAC1), while genes related to the gamma-aminobutyric acid (GABA) system were down-regulated (GABAA receptor, glutamate decarboxylase GAD65). Brain-derived neurotrophic factor (BDNF) was the only trophic factor whose gene was consistently up-regulated at all timepoints. These results, together with the fact that most of the genes up-regulated have a recognized interaction with BDNF, suggest a central role for BDNF on the effects of exercise on brain plasticity. The temporal profile of gene expression seems to delineate a mechanism by which specific molecular pathways are activated after exercise performance. For example, the CaM-K signal system seems to be active during acute and chronic periods of exercise, while the MAP-K/ERK system seems more important during long-term exercise. [source] Transcriptome analysis of Listeria monocytogenes identifies three groups of genes differently regulated by PrfAMOLECULAR MICROBIOLOGY, Issue 6 2003Eliane Milohanic Summary PrfA is the major regulator of Listeria virulence gene expression. This protein is a member of the Crp/Fnr family of transcription regulators. To gain a deeper understanding of the PrfA regulon, we constructed a whole-genome array based on the complete genome sequence of Listeria monocytogenes strain EGDe and evaluated the expression profiles of the wild-type EGDe and a prfA -deleted mutant (EGDe ,prfA). Both strains were grown at 37°C in brain,heart infusion broth (BHI) and BHI supplemented with either activated charcoal, a compound known to enhance virulence gene expression, or cellobiose, a sugar reported to downregulate virulence gene expression in spite of full expression of PrfA. We identified three groups of genes that are regulated differently. Group I comprises, in addition to the 10 already known genes, two new genes, lmo2219 and lmo0788, both positively regulated and preceded by a putative PrfA box. Group II comprises eight negatively regulated genes: lmo0278 is preceded by a putative PrfA box, and the remaining seven genes (lmo0178,lmo0184) are organized in an operon. Group III comprises 53 genes, of which only two (lmo0596 and lmo2067) are preceded by a putative PrfA box. Charcoal addition induced upregulation of group I genes but abolished regulation by PrfA of most group III genes. In the presence of cellobiose, all the group I genes were downregulated, whereas group III genes remained fully activated. Group II genes were repressed in all conditions tested. A comparison of the expression profiles between a second L. monocytogenes strain (P14), its spontaneous mutant expressing a constitutively active PrfA variant (P14prfA*) and its corresponding prfA -deleted mutant (P14,prfA) and the EGDe strain revealed interesting strain-specific differences. Sequences strongly similar to a sigma B-dependent promoter were identified upstream of 22 group III genes. These results suggest that PrfA positively regulates a core set of 12 genes preceded by a PrfA box and probably expressed from a sigma A-dependent promoter. In contrast, a second set of PrfA-regulated genes lack a PrfA box and are expressed from a sigma B-dependent promoter. This study reveals that PrfA can act as an activator or a repressor and suggests that PrfA may directly or indirectly activate different sets of genes in association with different sigma factors. [source] Structural mechanisms of multidrug recognition and regulation by bacterial multidrug transcription factorsMOLECULAR MICROBIOLOGY, Issue 4 2002Maria A. Schumacher Summary The increase in bacterial resistance to multiple drugs represents a serious and growing health risk. One component of multidrug resistance (MDR) is a group of multidrug transporters that are often regulated at the transcriptional level by repressors and/or activators. Some of these transcription factors are also multidrug-binding proteins, frequently recognizing the same array of drugs that are effluxed by the transporters that they regulate. How a single protein can recognize such chemically disparate compounds is an intriguing question from a structural standpoint and an important question in future drug development endeavours. Unlike the multidrug transporters, the cytosolic multidrug-binding regulatory proteins are more tractable systems for structural analyses. Here, we describe recent crystallographic studies on MarR, BmrR and QacR, three bacterial transcription regulators that are also multidrug-binding proteins. Although our understanding of multidrug binding and transcriptional regulation by MarR is in its initial stages, the structure of a BmrR,TPP+,DNA complex has revealed important insights into the novel transcription activation mechanism of the MerR family, and the structures of a QacR,DNA complex and QacR bound to six different drugs have revealed not only the mechanism of induction of this repressor but has afforded the first view of any MDR protein bound to multiple drugs. [source] Riboregulation by DsrA RNA: trans -actions for global economyMOLECULAR MICROBIOLOGY, Issue 4 2000MicroReview DsrA is an 87 nucleotide Escherichia coli RNA with extraordinary regulatory properties. The profound impact of its actions stems from DsrA regulating translation of two global transcription regulators, H-NS and RpoS (,s), by sequence-specific RNA,RNA interactions. H-NS is a major nucleoid-structuring and global repressor protein, and RpoS is the stationary phase and stress response sigma factor of RNA polymerase. DsrA changes its conformation to bind to these two different mRNA targets and thereby inhibits H-NS translation, while stimulating that of RpoS in a mechanistically distinct fashion. DsrA apparently binds both the start and the stop codons of hns mRNA and sharply decreases the mRNA half-life. DsrA also binds sequences in the 5,-untranslated leader region of rpoS mRNA, enhancing rpoS mRNA stability and RpoS translation. A cohort of genes, governed by H-NS repression and RpoS activation, are thus regulated. Low temperatures increase the levels of DsrA, with differential effects on H-NS and RpoS. Additionally, the RNA chaperone protein Hfq is involved with DsrA regulation, as well as with other small RNAs that also act on RpoS to co-ordinate stress responses. We address the possible functions of this genetic regulatory mechanism, as well as the advantages of using small RNAs as global regulators to orchestrate gene expression. [source] The X-ray crystal structure of PA1607 from Pseudomonas aureginosa at 1.9 Å resolution,a putative transcription factorPROTEIN SCIENCE, Issue 3 2007Edyta A.L. Sieminska Abstract The structure of the PA1607 protein from Pseudomonas aureginosa was determined at 1.85 Å resolution using the Se-Met multiwavelength anomalous diffraction (MAD) technique. PA1607 forms a dimer and adopts a winged-helix motif similar to the MarR family of transcription regulators, though it has an unusual dimerization profile. The DNA-binding regions and a putative metal-binding site are not conserved in PA1607. [source] Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+ -binding FCD domainsACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2009Meiying Zheng The GntR superfamily of dimeric transcription factors, with more than 6200 members encoded in bacterial genomes, are characterized by N-terminal winged-helix DNA-binding domains and diverse C-terminal regulatory domains which provide a basis for the classification of the constituent families. The largest of these families, FadR, contains nearly 3000 proteins with all-,-helical regulatory domains classified into two related Pfam families: FadR_C and FCD. Only two crystal structures of FadR-family members, those of Escherichia coli FadR protein and LldR from Corynebacterium glutamicum, have been described to date in the literature. Here, the crystal structure of TM0439, a GntR regulator with an FCD domain found in the Thermotoga maritima genome, is described. The FCD domain is similar to that of the LldR regulator and contains a buried metal-binding site. Using atomic absorption spectroscopy and Trp fluorescence, it is shown that the recombinant protein contains bound Ni2+ ions but that it is able to bind Zn2+ with Kd < 70,nM. It is concluded that Zn2+ is the likely physiological metal and that it may perform either structural or regulatory roles or both. Finally, the TM0439 structure is compared with two other FadR-family structures recently deposited by structural genomics consortia. The results call for a revision in the classification of the FadR family of transcription factors. [source] Form and function of dosage-compensated chromosomes , a chicken-and-egg relationshipBIOESSAYS, Issue 8 2010Charlotte Grimaud Abstract Does the three-dimensional (3D) conformation of interphase chromosomes merely reflect their function or does it actively contribute to gene regulation? The analysis of sex chromosomes that are subject to chromosome-wide dosage compensation processes promises new insight into this question. Chromosome conformations are dynamic and largely determined by association of distant chromosomal loci in the nuclear space or by their anchoring to the nuclear envelope, effectively generating chromatin loops. The type and extent of such interactions depend on chromatin-bound transcription regulators and therefore reflects function. Dosage compensation adjusts the overall transcription activity of X chromosomes to assure balanced expression in the two sexes. Initial analyses of mammalian and Drosophila X chromosomes have led to the hypothesis that their conformations may not only reflect their functional state but may in turn contribute to the coordination of chromosome-wide tuning of transcription. [source] Crystallization and preliminary crystallographic analysis of the global nitrogen regulator AmtR from Corynebacterium glutamicumACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2009Kristin Hasselt AmtR, a member of the TetR family of transcription regulators, is a global regulator of nitrogen control in Corynebacterium glutamicum. Unlike other TetR-family members, which are regulated by small-molecule effectors, AmtR is regulated by a protein called GlnK. It has been shown that a GlnK trimer has to become adenylylated prior to formation of a complex with AmtR. The physiological function of AmtR has been very well studied, but structural characterization of the mechanistic aspects of AmtR-regulated transcription has yet to be accomplished. AmtR has successfully been crystallized in space group P21212, with six molecules in the asymmetric unit and unit-cell parameters a = 153.34, b = 163.10, c = 51.93,Å. Preliminary phases were obtained using Se-SAD. [source] Structure of the apo form of the catabolite control protein A (CcpA) from Bacillus megaterium with a DNA-binding domainACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2007Rajesh Kumar Singh Crystal structure determination of catabolite control protein A (CcpA) at 2.6,Å resolution reveals for the first time the structure of a full-length apo-form LacI-GalR family repressor protein. In the crystal structures of these transcription regulators, the three-helix bundle of the DNA-binding domain has only been observed in cognate DNA complexes; it has not been observed in other crystal structures owing to its mobility. In the crystal packing of apo-CcpA, the protein,protein contacts between the N-terminal three-helix bundle and the core domain consisted of interactions between the homodimers that were similar to those between the corepressor protein HPr and the CcpA N-subdomain in the ternary DNA complex. In contrast to the DNA complex, the apo-CcpA structure reveals large subdomain movements in the core, resulting in a complete loss of contacts between the N-subdomains of the homodimer. [source] | |||||||||||||