scholarly journals Snail Upregulates Transcription of FN, LEF, COX2, and COL1A1 in Hepatocellular Carcinoma: A General Model Established for Snail to Transactivate Mesenchymal Genes

Cells ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 2202 ◽  
Author(s):  
Tam Minh Ly ◽  
Yen-Cheng Chen ◽  
Ming-Che Lee ◽  
Chi-Tan Hu ◽  
Chuan-Chu Cheng ◽  
...  
Keyword(s):  
General Model ◽  
Collagen Type ◽  
Site Directed Mutagenesis ◽  
Binding Motif ◽  
Deletion Mapping ◽  
Promoter Regions ◽  
Promoter Assay ◽  
Binding Factor ◽  
Luciferase Promoter Assay ◽  
Overlapping Region

SNA is one of the essential EMT transcriptional factors capable of suppressing epithelial maker while upregulating mesenchymal markers. However, the mechanisms for SNA to transactivate mesenchymal markers was not well elucidated. Recently, we demonstrated that SNA collaborates with EGR1 and SP1 to directly upregulate MMP9 and ZEB1. Remarkably, a SNA-binding motif (TCACA) upstream of EGR/SP1 overlapping region on promoters was identified. Herein, we examined whether four other mesenchymal markers, lymphoid enhancer-binding factor (LEF), fibronectin (FN), cyclooxygenase 2 (COX2), and collagen type alpha I (COL1A1) are upregulated by SNA in a similar fashion. Expectedly, SNA is essential for expression of these mesenchymal genes. By deletion mapping and site directed mutagenesis coupled with dual luciferase promoter assay, SNA-binding motif and EGR1/SP1 overlapping region are required for TPA-induced transcription of LEF, FN, COX2 and COL1A1. Consistently, TPA induced binding of SNA and EGR1/SP1 on relevant promoter regions of these mesenchymal genes using ChIP and EMSA. Thus far, we found six of the mesenchymal genes are transcriptionally upregulated by SNA in the same fashion. Moreover, comprehensive screening revealed similar sequence architectures on promoter regions of other SNA-upregulated mesenchymal markers, suggesting that a general model for SNA-upregulated mesenchymal genes can be established.

scholarly journals Snail upregulates FN and LEF transcription negatively feed backed by PPAR-gamma: a general model established for Snail to transactivate mesenchymal genes

2021 ◽  
Author(s):  
Tam Minh Ly ◽  
Yen-Cheng Chen ◽  
Ming-Che Lee ◽  
Chuan Chu Chen ◽  
Hsin-Hou Chang ◽  
...  
Keyword(s):  
General Model ◽  
Regulatory Region ◽  
Ppar Gamma ◽  
Luciferase Assay ◽  
Binding Motif ◽  
Deletion Mapping ◽  
Promoter Activation ◽  
Promoter Regions ◽  
Mesenchymal Transition ◽  
Overlapping Region

Abstract Background Snail (SNA) is responsible for epithelial mesenchymal transition, migration and metastasis of hepatocellular carcinoma. SNA represses the transcription of the essential epithelial marker such as E-cadherin and enhances mesenchymal markers including fibronectin and lymphoid enhancer-binding factor. Our previous studies indicated that SNA, in collaboration with EGR1 and SP1, may directly activate transcription of the mesenchymal markers, matrix degradation enzyme matrix metalloproteinases (MMP9) and zinc finger E-box binding homeobox 1 (ZEB1) in HepG2 cell stimulated by the phorbol ester tumor promoter 12-O-tetradecanoyl-phorbol 13-acetate (TPA). Besides, we pinpointed a SNA binding motif (TCACA) upstream of EGR1/SP1 overlapping region on promoters. In this study, we investigated whether LEF and FN are transcriptionally regulated by SNA in a similar fashion. Moreover, a general model for SNA-upregulated mesenchymal markers is proposed.Methods RT/PCR and Western blot were used for analyzing gene expression and shRNA technology for depleting SNA. Dual luciferase assay was used for promoter activation; deletion mapping and mutagenesis were used for confirming the indicated promoter region required for transcription activation. ChIP and EMSA were used for validating the binding of the indicated transcription factor on their putative motifs. Results SNA binding motif and E/S overlapping region are required for TPA-induced transcription of LEF and FN. These were supported by TPA-induced binding of SNA and EGR-1/SP-1 on indicated promoter regions. Moreover, a peroxisome proliferator-activated receptor γ motif upstream of SNA binding motif was found to be a negatively regulatory region in TPA-induced promoter activation of FN, LEF, MMP9 and ZEB1. This was supported by that co-treatment of a PPAR-g inhibitor, GW9662, and mutation of PPAR-g binding motif enhanced TPA-induced promoter activity and expression of the aforementioned genes whereas overexpression of PPAR-g reversed it. Moreover, comprehensive screening of the SNA-upregulated mesenchymal genes revealed similar sequence architecture on the promoter regions of the candidate genes: SNA binding motif (TCACA) coupled with a downstream EGR/SP1 overlapping region and an upstream PPAR-g binding motif. Among them COX2 and COL1A1 were found to potentially exhibit the same transcription mechanisms described above. Conclusions We established a general model for SNA-upregulated mesenchymal gene expressions negatively feed backed by PPAR-g.

scholarly journals Characterization of a New LexA Binding Motif in the Marine Magnetotactic Bacterium Strain MC-1

2003 ◽  
Vol 185 (15) ◽  
pp. 4471-4482 ◽  
Author(s):  
Antonio R. Fernández de Henestrosa ◽  
Jordi Cuñé ◽  
Gerard Mazón ◽  
Bradley L. Dubbels ◽  
Dennis A. Bazylinski ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Open Reading Frames ◽  
Site Directed Mutagenesis ◽  
Transcriptional Unit ◽  
Pcr Analysis ◽  
Binding Motif ◽  
Magnetotactic Bacterium ◽  
Promoter Regions ◽  
Mobility Shift ◽  
Lexa Protein

ABSTRACT MC-1 is a marine, magnetotactic bacterium that is phylogenetically associated with the alpha subclass of the Proteobacteria and is the first and only magnetotactic coccus isolated in pure culture to date. By using a TBLASTN search, a lexA gene was identified in the published genome of MC-1; it was subsequently cloned, and the protein was purified to >90% purity. Results from reverse transcription-PCR analysis revealed that the MC-1 lexA gene comprises a single transcriptional unit with two open reading frames encoding proteins of unknown function and with a rumA-like gene, a homologue of the Escherichia coli umuD gene. Mobility shift assays revealed that this LexA protein specifically binds both to its own promoter and to that of the umuDC operon. However, MC-1 LexA does not bind to the promoter regions of other genes, such as recA and uvrA, that have been previously reported to be regulated by LexA in bacterial species belonging to the alpha subclass of the Proteobacteria. Site-directed mutagenesis of both the lexA and umuDC operator regions demonstrated that the sequence CCTN10AGG is the specific target motif for the MC-1 LexA protein.

scholarly journals Structural and Functional Insights into Peptidoglycan Access for the Lytic Amidase LytA of Streptococcus pneumoniae

mBio ◽  
2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Peter Mellroth ◽  
Tatyana Sandalova ◽  
Alexey Kikhney ◽  
Francisco Vilaplana ◽  
Dusan Hesek ◽  
...  
Keyword(s):  
Cell Wall ◽  
Streptococcus Pneumoniae ◽  
Solution Structure ◽  
Substrate Binding ◽  
Substrate Recognition ◽  
Lytic Activity ◽  
Site Directed Mutagenesis ◽  
Binding Motif ◽  
Content Type ◽  
Peptidoglycan Synthesis

ABSTRACT The cytosolic N-acetylmuramoyl-l-alanine amidase LytA protein of Streptococcus pneumoniae, which is released by bacterial lysis, associates with the cell wall via its choline-binding motif. During exponential growth, LytA accesses its peptidoglycan substrate to cause lysis only when nascent peptidoglycan synthesis is stalled by nutrient starvation or β-lactam antibiotics. Here we present three-dimensional structures of LytA and establish the requirements for substrate binding and catalytic activity. The solution structure of the full-length LytA dimer reveals a peculiar fold, with the choline-binding domains forming a rigid V-shaped scaffold and the relatively more flexible amidase domains attached in a trans position. The 1.05-Å crystal structure of the amidase domain reveals a prominent Y-shaped binding crevice composed of three contiguous subregions, with a zinc-containing active site localized at the bottom of the branch point. Site-directed mutagenesis was employed to identify catalytic residues and to investigate the relative impact of potential substrate-interacting residues lining the binding crevice for the lytic activity of LytA. In vitro activity assays using defined muropeptide substrates reveal that LytA utilizes a large substrate recognition interface and requires large muropeptide substrates with several connected saccharides that interact with all subregions of the binding crevice for catalysis. We hypothesize that the substrate requirements restrict LytA to the sites on the cell wall where nascent peptidoglycan synthesis occurs. IMPORTANCE Streptococcus pneumoniae is a human respiratory tract pathogen responsible for millions of deaths annually. Its major pneumococcal autolysin, LytA, is required for autolysis and fratricidal lysis and functions as a virulence factor that facilitates the spread of toxins and factors involved in immune evasion. LytA is also activated by penicillin and vancomycin and is responsible for the lysis induced by these antibiotics. The factors that regulate the lytic activity of LytA are unclear, but it was recently demonstrated that control is at the level of substrate recognition and that LytA required access to the nascent peptidoglycan. The present study was undertaken to structurally and functionally investigate LytA and its substrate-interacting interface and to determine the requirements for substrate recognition and catalysis. Our results reveal that the amidase domain comprises a complex substrate-binding crevice and needs to interact with a large-motif epitope of peptidoglycan for catalysis.

Identification of an upstream regulatory sequence that mediates the transcription of mox genes in Methylobacterium extorquens AM1

Microbiology ◽  
2005 ◽  
Vol 151 (11) ◽  
pp. 3723-3728 ◽  
Author(s):  
Meng Zhang ◽  
Kelly A. FitzGerald ◽  
Mary E. Lidstrom
Keyword(s):  
Promoter Activity ◽  
Site Directed Mutagenesis ◽  
Regulatory Sequence ◽  
Methylobacterium Extorquens ◽  
Promoter Regions ◽  
Enhancer Element ◽  
Conserved Sequence ◽  
Normal Expression ◽  
Genetic Constructs ◽  
Transcriptional Fusions

A multiple A-tract sequence has been identified in the promoter regions for the mxaF, pqqA, mxaW, mxbD and mxcQ genes involved in methanol oxidation in Methylobacterium extorquens AM1, a facultative methylotroph. Site-directed mutagenesis was exploited to delete or change this conserved sequence. Promoter-xylE transcriptional fusions were used to assess promoter activity in these mutants. A fiftyfold drop in the XylE activity was observed for the mxaF and pqqA promoters without this sequence, and a five- to sixfold drop in the XylE activity was observed for the mxbD and mxcQ promoters without this sequence. Mutants were generated in the chromosomal copies in which this sequence was either deleted or altered, and these mutants were unable to grow on methanol. When one of these sequences was added to Plac of Escherichia coli, which is a weak constitutive promoter in M. extorquens AM1, the activity increased two- to threefold. These results suggest that this sequence is essential for normal expression of these genes in M. extorquens AM1, and may serve as a general enhancer element for genetic constructs in this bacterium.

scholarly journals Identification of amino acids essential for DNA binding and dimerization in p67SRF: implications for a novel DNA-binding motif

1993 ◽  
Vol 13 (1) ◽  
pp. 123-132
Author(s):  
A D Sharrocks ◽  
H Gille ◽  
P E Shaw
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Dna Binding ◽  
Transcriptional Activation ◽  
Serum Response Factor ◽  
Alpha Helix ◽  
Site Directed Mutagenesis ◽  
Binding Motif ◽  
Amino Acid Peptide ◽  
Serum Response

The serum response factor (p67SRF) binds to a palindromic sequence in the c-fos serum response element (SRE). A second protein, p62TCF binds in conjunction with p67SRF to form a ternary complex, and it is through this complex that growth factor-induced transcriptional activation of c-fos is thought to take place. A 90-amino-acid peptide, coreSRF, is capable for dimerizing, binding DNA, and recruiting p62TCF. By using extensive site-directed mutagenesis we have investigated the role of individual coreSRF amino acids in DNA binding. Mutant phenotypes were defined by gel retardation and cross-linking analyses. Our results have identified residues essential for either DNA binding or dimerization. Three essential basic amino acids whose conservative mutation severely reduced DNA binding were identified. Evidence which is consistent with these residues being on the face of a DNA binding alpha-helix is presented. A phenylalanine residue and a hexameric hydrophobic box are identified as essential for dimerization. The amino acid phasing is consistent with the dimerization interface being presented as a continuous region on a beta-strand. A putative second alpha-helix acts as a linker between these two regions. This study indicates that p67SRF is a member of a protein family which, in common with many DNA binding proteins, utilize an alpha-helix for DNA binding. However, this alpha-helix is contained within a novel domain structure.

scholarly journals Characterization of the SOS Regulon of Caulobacter crescentus

2007 ◽  
Vol 190 (4) ◽  
pp. 1209-1218 ◽  
Author(s):  
Raquel Paes da Rocha ◽  
Apuã César de Miranda Paquola ◽  
Marilis do Valle Marques ◽  
Carlos Frederico Martins Menck ◽  
Rodrigo S. Galhardo
Keyword(s):  
Dna Damage ◽  
Caulobacter Crescentus ◽  
Bacterial Species ◽  
Direct Repeat ◽  
Site Directed Mutagenesis ◽  
Dependent Manner ◽  
Wild Type ◽  
Promoter Regions ◽  
Potential Promoter

ABSTRACT The SOS regulon is a paradigm of bacterial responses to DNA damage. A wide variety of bacterial species possess homologs of lexA and recA, the central players in the regulation of the SOS circuit. Nevertheless, the genes actually regulated by the SOS have been determined only experimentally in a few bacterial species. In this work, we describe 37 genes regulated in a LexA-dependent manner in the alphaproteobacterium Caulobacter crescentus. In agreement with previous results, we have found that the direct repeat GTTCN7GTTC is the SOS operator of C. crescentus, which was confirmed by site-directed mutagenesis studies of the imuA promoter. Several potential promoter regions containing the SOS operator were identified in the genome, and the expression of the corresponding genes was analyzed for both the wild type and the lexA strain, demonstrating that the vast majority of these genes are indeed SOS regulated. Interestingly, many of these genes encode proteins with unknown functions, revealing the potential of this approach for the discovery of novel genes involved in cellular responses to DNA damage in prokaryotes, and illustrating the diversity of SOS-regulated genes among different bacterial species.

scholarly journals Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki

2018 ◽  
Vol 115 (10) ◽  
pp. E2477-E2486 ◽  
Author(s):  
Pavel V. Mazin ◽  
Elena Shagimardanova ◽  
Olga Kozlova ◽  
Alexander Cherkasov ◽  
Roman Sutormin ◽  
...  
Keyword(s):  
Heat Shock ◽  
Gene Activation ◽  
Regulatory System ◽  
Late Embryogenesis Abundant ◽  
Binding Motif ◽  
Transcription Activator ◽  
Promoter Regions ◽  
Genes Encoding ◽  
Polypedilum Vanderplanki ◽  
The Sleeping Chironomid

Polypedilum vanderplanki is a striking and unique example of an insect that can survive almost complete desiccation. Its genome and a set of dehydration–rehydration transcriptomes, together with the genome of Polypedilum nubifer (a congeneric desiccation-sensitive midge), were recently released. Here, using published and newly generated datasets reflecting detailed transcriptome changes during anhydrobiosis, as well as a developmental series, we show that the TCTAGAA DNA motif, which closely resembles the binding motif of the Drosophila melanogaster heat shock transcription activator (Hsf), is significantly enriched in the promoter regions of desiccation-induced genes in P. vanderplanki, such as genes encoding late embryogenesis abundant (LEA) proteins, thioredoxins, or trehalose metabolism-related genes, but not in P. nubifer. Unlike P. nubifer, P. vanderplanki has double TCTAGAA sites upstream of the Hsf gene itself, which is probably responsible for the stronger activation of Hsf in P. vanderplanki during desiccation compared with P. nubifer. To confirm the role of Hsf in desiccation-induced gene activation, we used the Pv11 cell line, derived from P. vanderplanki embryo. After preincubation with trehalose, Pv11 cells can enter anhydrobiosis and survive desiccation. We showed that Hsf knockdown suppresses trehalose-induced activation of multiple predicted Hsf targets (including P. vanderplanki-specific LEA protein genes) and reduces the desiccation survival rate of Pv11 cells fivefold. Thus, cooption of the heat shock regulatory system has been an important evolutionary mechanism for adaptation to desiccation in P. vanderplanki.

Activation Control of pur Gene Expression inLactococcus lactis: Proposal for a Consensus Activator Binding Sequence Based on Deletion Analysis and Site-Directed Mutagenesis of purC and purD Promoter Regions

1998 ◽  
Vol 180 (15) ◽  
pp. 3900-3906 ◽  
Author(s):  
Mogens Kilstrup ◽  
Stine G. Jessing ◽  
Stephanie B. Wichmand-Jørgensen ◽  
Mette Madsen ◽  
Dan Nilsson
Keyword(s):  
Site Directed Mutagenesis ◽  
Deletion Analysis ◽  
Directed Mutagenesis ◽  
Promoter Regions ◽  
Conserved Sequence ◽  
Similar Region ◽  
Low Levels ◽  
High Level ◽  
Transcriptional Start Sites ◽  
Binding Sequence

ABSTRACT A comparison of the purC and purD upstream regions from Lactococcus lactis revealed the presence of a conserved ACCGAACAAT decanucleotide sequence located precisely between −79 and −70 nucleotides upstream from the transcriptional start sites. Both promoters have well-defined −10 regions but lack sequences resembling −35 regions for ς70 promoters. Fusion studies indicated the importance of the conserved sequence in purine-mediated regulation. Adjacent to the conserved sequence in purC is a second and similar region required for high-level expression of the gene. A consensus PurBox sequence (AWWWCCGAACWWT) could be proposed for the three regions. By site-directed mutagenesis we found that mutation of the central G in the PurBox sequence to C resulted in low levels of transcription and the loss of purine-mediated regulation at thepurC and purD promoters. Deletion analysis also showed that the nucleotides before the central CCGAAC core in the PurBox sequence are important. All results support the idea thatpurC and purD transcription is regulated by a transcriptional activator binding to the PurBox sequence.

scholarly journals Identification of Tyrosinase-related Protein 2 as a Tumor Rejection Antigen for the B16 Melanoma

1997 ◽  
Vol 185 (3) ◽  
pp. 453-460 ◽  
Author(s):  
Matthew B. Bloom ◽  
Donna Perry-Lalley ◽  
Paul F. Robbins ◽  
Yong Li ◽  
Mona El-Gamil ◽  
...  
Keyword(s):  
Normal Tissue ◽  
Tumor Antigens ◽  
Human Tumor ◽  
Human Melanoma ◽  
Tissue Differentiation ◽  
B16 Melanoma ◽  
Tumor Rejection ◽  
Site Directed Mutagenesis ◽  
Preclinical Model ◽  
Binding Motif

Recently, major advances have been made in the identification of antigens from human melanoma which are recognized by T cells. In spite of this, little is known about the optimal ways to use these antigens to treat patients with cancer. Progress in this area is likely to require accurate preclinical animal models, but the availability of such models has lagged behind developments in human tumor immunology. Whereas many of the identified human melanoma antigens are normal tissue differentiation proteins, analogous murine tumor antigens have not yet been identified. In this paper we identify a normal tissue differentiation antigen, tyrosinaserelated protein 2 (TRP-2), expressed by the murine B16 melanoma which was found by screening a cDNA library from B16 with tumor-reactive cytotoxic T lymphocytes (CTL). A peptide conforming to the predicted MHC class I H2-Kb binding motif, TRP-2181-188, was identified as the major reactive epitope within TRP-2 recognized by these anti-B16 CTLs. By site-directed mutagenesis, it was shown that alteration of this epitope eliminated recognition of TRP-2. It was further demonstrated that a CTL line raised from splenocytes by repeated stimulation in vitro with this peptide could recognize B16 tumor and was therapeutic against 3-d-old established pulmonary metastases. The use of TRP-2 in a preclinical model of tumor immunotherapy may be helpful in suggesting optimal vaccination strategies for cancer therapy in patients.

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