scholarly journals Analysis of the Promoter Region, Motif and CpG Islands in AraC Family Transcriptional Regulator ACP92 Genes of <i>Herbaspirillum seropedicae</i>

2019 ◽  
Vol 10 (06) ◽  
pp. 150-164
Author(s):  
Mihret Yirgu ◽  
Mulugeta Kebede
Keyword(s):  
Promoter Region ◽  
Cpg Islands ◽  
Transcriptional Regulator ◽  
Herbaspirillum Seropedicae ◽  
Arac Family

scholarly journals Transcriptional Regulation of the Nitrile Hydratase Gene Cluster in Pseudomonas chlororaphis B23

2008 ◽  
Vol 190 (12) ◽  
pp. 4210-4217 ◽  
Author(s):  
Toshihide Sakashita ◽  
Yoshiteru Hashimoto ◽  
Ken-Ichi Oinuma ◽  
Michihiko Kobayashi
Keyword(s):  
Gene Cluster ◽  
Nitrile Hydratase ◽  
Transcriptional Regulator ◽  
Pseudomonas Chlororaphis ◽  
Reading Frame ◽  
Transcription Start Sites ◽  
Reverse Transcription Pcr ◽  
Enormous Amount ◽  
Extension Analysis ◽  
Arac Family

ABSTRACT An enormous amount of nitrile hydratase (NHase) is inducibly produced by Pseudomonas chlororaphis B23 after addition of methacrylamide as the sole nitrogen source to a medium. The expression pattern of the P. chlororaphis B23 NHase gene cluster in response to addition of methacrylamide to the medium was investigated. Recently, we reported that the NHase gene cluster comprises seven genes (oxdA, amiA, nhpA, nhpB, nhpC, nhpS, and acsA). Sequence analysis of the 1.5-kb region upstream of the oxdA gene revealed the presence of a 936-bp open reading frame (designated nhpR), which should encode a protein with a molecular mass of 35,098. The deduced amino acid sequence of the nhpR product showed similarity to the sequences of transcriptional regulators belonging to the XylS/AraC family. Although the transcription of the eight genes (nhpR, oxdA, amiA, nhpABC, nhpS, and acsA) in the NHase gene cluster was induced significantly in the P. chlororaphis B23 wild-type strain after addition of methacrylamide to the medium, transcription of these genes in the nhpR disruptant was not induced, demonstrating that nhpR codes for a positive transcriptional regulator in the NHase gene cluster. A reverse transcription-PCR experiment revealed that five genes (oxdA, amiA, nhpA, nhpB, and nhpC) are cotranscribed, as are two other genes (nhpS and acsA). The transcription start sites for nhpR, oxdA, nhpA, and nhpS were mapped by primer extension analysis, and putative −12 and −24 σ54-type promoter binding sites were identified. NhpR was found to be the first transcriptional regulator of NHase belonging to the XylS/AraC family.

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 The mechanism of MYB transcriptional regulation by MLL-AF9 oncoprotein

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Lu Cao ◽  
Partha Mitra ◽  
Thomas J. Gonda
Keyword(s):  
Cell Proliferation ◽  
Transcriptional Regulation ◽  
Acute Myeloid Leukaemia ◽  
Promoter Region ◽  
Transcriptional Regulator ◽  
Transcriptional Regulators ◽  
Therapeutic Approaches ◽  
New Therapeutic Approaches ◽  
H3k79 Methylation ◽  
Acute Myeloid

AbstractAcute leukaemias express high levels of MYB which are required for the initiation and maintenance of the disease. Inhibition of MYB expression or activity has been shown to suppress MLL-fusion oncoprotein-induced acute myeloid leukaemias (AML), which are among the most aggressive forms of AML, and indeed MYB transcription has been reported to be regulated by the MLL-AF9 oncoprotein. This highlights the importance of understanding the mechanism of MYB transcriptional regulation in these leukaemias. Here we have demonstrated that the MLL-AF9 fusion protein regulates MYB transcription directly at the promoter region, in part by recruiting the transcriptional regulator kinase CDK9, and CDK9 inhibition effectively suppresses MYB expression as well as cell proliferation. However, MYB regulation by MLL-AF9 does not require H3K79 methylation mediated by the methyltransferase DOT1L, which has also been shown to be a key mediator of MLL-AF9 leukemogenicity. The identification of specific, essential and druggable transcriptional regulators may enable effective targeting of MYB expression, which in turn could potentially lead to new therapeutic approaches for acute myeloid leukaemia with MLL-AF9.

scholarly journals Regulation of vanillate and syringate catabolism by a MarR-type transcriptional regulator DesR in Sphingobium sp. SYK-6

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Takuma Araki ◽  
Shusuke Umeda ◽  
Naofumi Kamimura ◽  
Daisuke Kasai ◽  
Shuta Kumano ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Dna Binding ◽  
Promoter Region ◽  
Transcriptional Regulator ◽  
Ring Cleavage ◽  
Effector Molecules ◽  
Repeat Sequences ◽  
Reverse Transcription Pcr ◽  
Consecutive Reactions ◽  
Intermediate Metabolites

AbstractVanillate and syringate are major intermediate metabolites generated during the microbial degradation of lignin. In Sphingobium sp. SYK-6, vanillate is O demethylated to protocatechuate by LigM; protocatechuate is then catabolized via the protocatechuate 4,5-cleavage pathway. Syringate is O demethylated to gallate by consecutive reactions catalyzed by DesA and LigM, and then gallate is subjected to ring cleavage by DesB. Here, we investigated the transcriptional regulation of desA, ligM, and desB involved in vanillate and syringate catabolism. Quantitative reverse transcription-PCR analyses indicated that the transcription of these genes was induced 5.8–37-fold in the presence of vanillate and syringate. A MarR-type transcriptional regulator, SLG_12870 (desR), was identified as the gene whose product bound to the desB promoter region. Analysis of a desR mutant indicated that the transcription of desB, ligM, and desR is negatively regulated by DesR. Purified DesR bound to the upstream regions of desB, ligM, and desR, and the inverted repeat sequences similar to each other in these regions were suggested to be essential for DNA binding of DesR. Vanillate and syringate inhibited DNA binding of DesR, indicating that these compounds are effector molecules of DesR. The transcription of desA was found to be regulated by an as-yet unidentified regulator.

Fucose-Mediated Transcriptional Activation of the fcs Operon by FcsR in Streptococcus pneumoniae

2015 ◽  
Vol 25 (2-3) ◽  
pp. 120-128 ◽  
Author(s):  
Irfan Manzoor ◽  
Sulman Shafeeq ◽  
Muhammad Afzal ◽  
Oscar P. Kuipers
Keyword(s):  
Streptococcus Pneumoniae ◽  
Transcriptional Activation ◽  
Promoter Region ◽  
Transcriptional Regulator ◽  
Transcriptional Activator ◽  
Regulatory Site ◽  
Rt Pcr ◽  
The Impact

In this study, we explore the impact of fucose on the transcriptome of <i>S. pneumoniae</i> D39. The expression of various genes and operons, including the fucose uptake PTS and utilization operon (<i>fcs</i> operon) was altered in the presence of fucose. By means of quantitative RT-PCR and β-galactosidase analysis, we demonstrate the role of the transcriptional regulator FcsR, present upstream of the <i>fcs</i> operon, as a transcriptional activator of the <i>fcs</i> operon. We also predict a 19-bp putative FcsR regulatory site (5′-ATTTGAACATTATTCAAGT-3′) in the promoter region of the <i>fcs</i> operon. The functionality of this predicted FcsR regulatory site was further confirmed by promoter-truncation experiments, where deletion of half of the FscR regulatory site or full deletion led to the abolition of expression of the <i>fcs</i> operon.

scholarly journals Genetic and Transcriptional Organization of the clpC Locus in Bifidobacterium breve UCC 2003

2005 ◽  
Vol 71 (10) ◽  
pp. 6282-6291 ◽  
Author(s):  
Marco Ventura ◽  
Gerald F. Fitzgerald ◽  
Douwe van Sinderen
Keyword(s):  
Promoter Region ◽  
Specific Binding ◽  
Transcriptional Regulator ◽  
Biologically Active ◽  
Slot Blot ◽  
Bifidobacterium Breve ◽  
Homologous Genes ◽  
Species Analysis ◽  
Atpase Gene

ABSTRACT A homolog of the clpC ATPase gene was identified in the genome of Bifidobacterium breve UCC 2003. Since this gene is very well conserved among eubacteria, we employed a PCR-based approach using primers based on highly conserved regions of ClpC proteins in order to identify homologous genes in other bifidobacterial species. Analysis by slot blot, Northern blot, and primer extension experiments showed that transcription of clpC is induced in response to moderate heat shock regimes. Moreover, we identified in the genome sequence of B. breve UCC 2003 a gene, designated clgR, which is predicted to encode a transcriptional regulator involved in regulation of the bifidobacterial clpC gene. The role of this protein in the regulation of B. breve UCC 2003 clpC gene expression was investigated by performing gel retardation experiments. We show that a biologically active ClgR molecule requires one or more proteinaceous coactivators to assist in the specific binding of ClgR to the clpC promoter region.

scholarly journals Regulation of Lactobacillus casei Sorbitol Utilization Genes Requires DNA-Binding Transcriptional Activator GutR and the Conserved Protein GutM

2008 ◽  
Vol 74 (18) ◽  
pp. 5731-5740 ◽  
Author(s):  
Cristina Alcántara ◽  
Luz Adriana Sarmiento-Rubiano ◽  
Vicente Monedero ◽  
Josef Deutscher ◽  
Gaspar Pérez-Martínez ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Sequence Comparison ◽  
Promoter Region ◽  
Lactobacillus Casei ◽  
Transcriptional Regulator ◽  
Transcriptional Activator ◽  
Regulation Mechanism ◽  
Phosphotransferase System ◽  
Footprint Analysis ◽  
Operon Expression

ABSTRACT Sequence analysis of the five genes (gutRMCBA) downstream from the previously described sorbitol-6-phosphate dehydrogenase-encoding Lactobacillus casei gutF gene revealed that they constitute a sorbitol (glucitol) utilization operon. The gutRM genes encode putative regulators, while the gutCBA genes encode the EIIC, EIIBC, and EIIA proteins of a phosphoenolpyruvate-dependent sorbitol phosphotransferase system (PTSGut). The gut operon is transcribed as a polycistronic gutFRMCBA messenger, the expression of which is induced by sorbitol and repressed by glucose. gutR encodes a transcriptional regulator with two PTS-regulated domains, a galactitol-specific EIIB-like domain (EIIBGat domain) and a mannitol/fructose-specific EIIA-like domain (EIIAMtl domain). Its inactivation abolished gut operon transcription and sorbitol uptake, indicating that it acts as a transcriptional activator. In contrast, cells carrying a gutB mutation expressed the gut operon constitutively, but they failed to transport sorbitol, indicating that EIIBCGut negatively regulates GutR. A footprint analysis showed that GutR binds to a 35-bp sequence upstream from the gut promoter. A sequence comparison with the presumed promoter region of gut operons from various firmicutes revealed a GutR consensus motif that includes an inverted repeat. The regulation mechanism of the L. casei gut operon is therefore likely to be operative in other firmicutes. Finally, gutM codes for a conserved protein of unknown function present in all sequenced gut operons. A gutM mutant, the first constructed in a firmicute, showed drastically reduced gut operon expression and sorbitol uptake, indicating a regulatory role also for GutM.

scholarly journals Construction and Use of an ipb DNA Module To Generate Pseudomonas Strains with Constitutive Trichloroethene and Isopropylbenzene Oxidation Activity

1998 ◽  
Vol 64 (7) ◽  
pp. 2454-2462 ◽  
Author(s):  
Frank Berendes ◽  
Nicolas Sabarth ◽  
Beate Averhoff ◽  
Gerhard Gottschalk
Keyword(s):  
Dna Sequences ◽  
Promoter Region ◽  
Sequence Similarity ◽  
Regulatory Protein ◽  
Continuous Cultivation ◽  
Oxidation Activity ◽  
Translational Initiation ◽  
Degradation Rates ◽  
Tce Degradation ◽  
Arac Family

ABSTRACT Pseudomonas sp. strain JR1 exhibits trichloroethene (TCE) oxidation activity with isopropylbenzene (IPB) as the inducer substrate. We previously reported the genes encoding the first three enzymes of the IPB-degradative pathway (ipbA1,ipbA2, ipbA3, ipbA4,ipbB, and ipbC) and identified the initial IPB dioxygenase (IpbA1A2A3A4) as responsible for TCE cooxidation (U. Pflugmacher, B. Averhoff, and G. Gottschalk, Appl. Environ. Microbiol. 62:3967–3977, 1996). Primer extension analyses revealed multiple transcriptional start points located upstream of the translational initiation codon of ipbA1. The transcription from these start sites was found to be IPB dependent. Thirty-one base pairs upstream of the first transcriptional start point tandemly repeated DNA sequences overlapping the −35 region of a putative ς70 promoter were found. These repeats exhibit significant sequence similarity to the operator-promoter region of thexyl meta operon in Pseudomonas putida, which is required for the binding of XylS, a regulatory protein of the XylS (also called AraC) family. These similarities suggest that the transcription of the IPB dioxygenase genes is modulated by a regulatory protein of the XylS/AraC family. The construction of an ipbDNA module devoid of this ipb operator-promoter region and the stable insertion of this DNA module into the genomes of differentPseudomonas strains resulted in pseudomonads with constitutive IPB and TCE oxidation activities. Constitutive TCE oxidation of two such Pseudomonas hybrid strains, JR1A::ipb and CBS-3::ipb, was found to be stable for more than 120 generations in antibiotic-free medium. Evaluation of constitutive TCE degradation rates revealed that continuous cultivation of strain JR1A::ipbresulted in a significant increase in rates of TCE degradation.

Methylation of CpG Islands Was Involved in the Down-Regulation of DAZAP2 in Multiple Meyloma Cells.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 4157-4157
Author(s):  
Wei-Xin Hu ◽  
Wei Ren ◽  
Le-Qi He ◽  
Rong Sheng ◽  
Yi-Wu Shi
Keyword(s):  
Multiple Myeloma ◽  
Bone Marrow ◽  
Tumor Suppressor ◽  
Western Blot ◽  
Promoter Methylation ◽  
Promoter Region ◽  
Cpg Islands ◽  
Luciferase Reporter ◽  
Rt Pcr ◽  
Normal Controls

Abstract Our previous studies showed that DAZAP2 (deleted in azoospermia associated protein 2) was the most profoundly downregulated gene in bone marrow mononuclear cells from multiple meyloma (MM) patients. The results implicated a role for DAZAP2 as a potential tumor suppressor involved in the origin and development of MM. To further understand the molecular mechanism underlying this deregulation, we analyzed epigenetic changes (i.e., DNA methylation) associated with DAZAP2 in MM, given that aberrant promoter methylation contributes to tumorigenesis through inducing transcriptional suppression and tumor suppressor inactivation. Bioinformatics analysis showed that there are three CpG islands in the DAZAP2 promoter region. The fragments of DAZAP2 promoter region with different length were separately PCR-amplified and inserted into the luciferase reporter, pGL2-Basic vector. The reporter constructs were transfected into COS-7 cells and their luciferase activities measured. The results showed that the fragment containing the third CpG island was the most active among the constructs tested. When this fragment was treated with M. Sss I methylase, its luciferase activity was almost lost. On the other hand, after 5-aza-2′-deoxycytidine treatment, the expression of DAZAP2 was restored in KM3 cells, an MM cell line associated with DAZAP2 downregulation. To extend these observations, bone marrow samples from MM patients and normal controls were collected and genomic DNA, RNA and proteins were extracted from each sample for RT-PCR, MSP (methylation-specific PCR) and Western blot analyses. The results were in general agreement with that reported previously, demonstrating that the protein and mRNA of DAZAP2, while detectable in 100% normal controls, were undetectable in 62.5% MM patients. The MSP data further corroborated with RT-PCR and Western blot analysis (94%), which is characterized by a negative correlation between promoter methylation and downregulation of DAZAP2 in multiple myeloma. These results indicate that promoter hypermethylation may play an important role in downregulation of DAZAP2 gene expression in multiple myeloma.

Sign in / Sign up

Export Citation Format

Share Document