Genetic dissection of independent and cooperative transcriptional activation by the LysR-type activator ThnR at close divergent promoters

ABSTRACT Oxygen controls competence development in Streptococcus pneumoniae. Oxygen signaling involves the two-component signal transduction systems CiaRH and ComDE and the competence-stimulating peptide encoded by comC and processed by ComAB. We found that NADH oxidase (Nox) was required for optimal competence. Transcriptional analysis and genetic dissection showed that Nox was involved in post-transcriptional activation of the response regulator ComE and in the transcriptional control of ciaRH andcomCDE. Thus, in S. pneumoniae, Nox, with O2 as its secondary substrate, is part of the O2-signaling pathway.

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Identification of eQTL and sQTL associated with meat quality in beef

10.21203/rs.2.15326/v1 ◽

2019 ◽

Author(s):

Joel David Leal Gutierrez ◽

Mauricio A. Elzo ◽

Raluca G. Mateescu

Keyword(s):

Qtl Mapping ◽

Meat Quality ◽

Transcriptional Activation ◽

Network Architecture ◽

R Package ◽

Cytoskeletal Proteins ◽

Genetic Dissection ◽

Rna Seq ◽

Master Regulators ◽

Longissimus Dorsi Muscle

Abstract Background: Transcription has a substantial genetic control and genetic dissection of gene expression could help us understand the genetic architecture of complex phenotypes such as meat quality in cattle.Results: A total of 80 steers were selected for phenotyping, genotyping and RNA-seq evaluation. A panel of traits related to meat quality were recorded. Information on 112,042 SNPs and expression data on 8,588 autosomal genes and 87,770 exons from 8,467 genes were included in an expression and splicing quantitative trait loci (QTL) mapping (eQTL and sQTL, respectively). Expression of 1,352 genes was previously identified as associated with meat quality traits using a gene, exon and isoform differential expression (DE) analysis. The R package Matrix eQTL was used to perform the QTL mapping using linear regression. The identified QTLs were classified as cis or trans using 1 Mb as maximum distance between the associated SNP and the gene. Polymorphisms associated with expression of at least 20 genes, and splicing of at least 20 exons were considered QTL hot spots. A total of 8,377 eQTLs were identified, including 75.6% trans, 10.4% cis, 12.5% DE trans and 1.5% DE cis; 11,929 sQTLs were uncovered: 66.1% trans, 16.9% DE trans, 14% cis and 3% DE cis. Twenty seven expression master regulators and 13 splicing master regulators were identified and were classified as membrane associated or cytoskeletal proteins, transcription factors or DNA methylases These genes could control expression of other genes through cell signaling or by a direct transcriptional activation/repression mechanism. The ZNF804A, ALAD, OR13F1 and ENSBTAG00000000336 genes were identified as both expression and splicing master regulators.Conclusion: In the present analysis, we show that eQTL and sQTL mapping makes possible positional identification of gene and isoform expression regulators. Additionally, this mapping provides new insight into the regulatory network architecture in longissimus dorsi muscle in an Angus-Brahman multibreed population.

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AR1 Is an Integral Part of the Adenovirus Type 2 E1A-CR3 Transactivation Domain

Journal of Virology ◽

10.1128/jvi.72.7.5978-5983.1998 ◽

1998 ◽

Vol 72 (7) ◽

pp. 5978-5983 ◽

Cited By ~ 12

Author(s):

Anne-Christine Ström ◽

Petra Ohlsson ◽

Göran Akusjärvi

Keyword(s):

Amino Acid ◽

Transcriptional Activation ◽

Adenovirus Type ◽

Genetic Dissection ◽

Transactivation Domain ◽

Sequence Elements ◽

Carboxy Terminal ◽

Adenovirus Type 2

ABSTRACT We have previously shown that the nonconserved carboxy-terminal exon of the adenovirus type 2 E1A-289R protein contains two interchangeable sequence elements, auxiliary region (AR) 1 and AR2, that are required for efficient CR3-mediated transcriptional activation of the viral E4 promoter (M. Bondesson, C. Svensson, S. Linder, and G. Akusjärvi, EMBO J. 11:3347–3354, 1992). Here we show that CR3-mediated transactivation of all adenovirus early promoters and the HSP70 promoter requires the AR1 element. We further show that AR2 can substitute for AR1 only when artificially juxtaposed to CR3. AR1 consists of six tandem glutamic acid-proline (EP) repeats and is positioned immediately downstream of CR3. Genetic dissection of AR1 showed that the number of EP repeats in AR1 is critical for CR3 function. Thus, reducing or increasing the number of EP repeats reduces the CR3 transactivation capacity. Furthermore, the introduction of amino acid substitutions into AR1 suggested that the net negative charge in AR1 is of critical importance for its function as an enhancer of CR3-mediated transcriptional activation. Using an in vitro binding approach, we showed that the AR1 element is not part of the CR3 promoter localization signal mediating contact with the Sp1, ATF-2, or c-Jun upstream-binding transcription factors. Previous studies have suggested that the 49-amino-acid sequence constituting CR3 represents the minimal domain required for E1A-induced activation of viral early promoters. Since AR1 was required for efficient CR3-mediated transcriptional activation of all tested promoters, we suggest that the carboxy-terminal boundary for the CR3 transactivation domain should be extended to include the AR1 element.

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Multiple changes underlie allelic divergence of CUP2 between Saccharomyces species

10.1101/728980 ◽

2019 ◽

Author(s):

Xueying C. Li ◽

Justin C. Fay

Keyword(s):

Transcriptional Activation ◽

Copper Resistance ◽

Proximal Promoter ◽

Genetic Dissection ◽

Copper Binding ◽

Protein Coding ◽

Transcriptional Activation Domain ◽

Promoter Dna ◽

Nucleotide Resolution ◽

Distal Promoter

AbstractUnder the model of micromutationism, phenotypic divergence between species is caused by accumulation of many small-effect changes. While mapping the causal changes to single nucleotide resolution could be difficult for diverged species, genetic dissection via chimeric constructs allows us to evaluate whether a large-effect gene is composed of many small-effect nucleotide changes. In a previously described non-complementation screen, we found allele difference of CUP2, a copper-binding transcription factor, underlie divergence in copper resistance between Saccharomyces cerevisiae and S. uvarum. Here, we tested whether the allele effect of CUP2 was caused by multiple nucleotide changes. By analyzing chimeric constructs containing four separate regions in the CUP2 gene, including its distal promoter, proximal promoter, DNA binding domain and transcriptional activation domain, we found that all four regions of the S. cerevisiae allele conferred copper resistance, with the proximal promoter showing the largest effect, and that both additive and epistatic effects are likely involved. These findings support a model of multiple changes underlying evolution and suggest an important role of both protein coding and cis-regulatory changes in evolution.

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Copper-dependent ATP7B up-regulation drives the resistance of TMEM16A-overexpressing head-and-neck cancer models to platinum toxicity

Biochemical Journal ◽

10.1042/bcj20190591 ◽

2019 ◽

Vol 476 (24) ◽

pp. 3705-3719 ◽

Cited By ~ 2

Author(s):

Avani Vyas ◽

Umamaheswar Duvvuri ◽

Kirill Kiselyov

Keyword(s):

Oxidative Stress ◽

Head And Neck ◽

Transcriptional Activation ◽

Platinum Resistance ◽

Mrna Levels ◽

Strong Positive Correlation ◽

Platinum Compounds ◽

Copper Chelation ◽

Novel Approach ◽

Cancer Models

Platinum-containing drugs such as cisplatin and carboplatin are routinely used for the treatment of many solid tumors including squamous cell carcinoma of the head and neck (SCCHN). However, SCCHN resistance to platinum compounds is well documented. The resistance to platinum has been linked to the activity of divalent transporter ATP7B, which pumps platinum from the cytoplasm into lysosomes, decreasing its concentration in the cytoplasm. Several cancer models show increased expression of ATP7B; however, the reason for such an increase is not known. Here we show a strong positive correlation between mRNA levels of TMEM16A and ATP7B in human SCCHN tumors. TMEM16A overexpression and depletion in SCCHN cell lines caused parallel changes in the ATP7B mRNA levels. The ATP7B increase in TMEM16A-overexpressing cells was reversed by suppression of NADPH oxidase 2 (NOX2), by the antioxidant N-Acetyl-Cysteine (NAC) and by copper chelation using cuprizone and bathocuproine sulphonate (BCS). Pretreatment with either chelator significantly increased cisplatin's sensitivity, particularly in the context of TMEM16A overexpression. We propose that increased oxidative stress in TMEM16A-overexpressing cells liberates the chelated copper in the cytoplasm, leading to the transcriptional activation of ATP7B expression. This, in turn, decreases the efficacy of platinum compounds by promoting their vesicular sequestration. We think that such a new explanation of the mechanism of SCCHN tumors’ platinum resistance identifies novel approach to treating these tumors.

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Role of molecular chaperones in steroid receptor action

Essays in Biochemistry ◽

10.1042/bse0400041 ◽

2004 ◽

Vol 40 ◽

pp. 41-58 ◽

Cited By ~ 149

Author(s):

William B Pratt ◽

Mario D Galigniana ◽

Yoshihiro Morishima ◽

Patrick J M Murphy

Keyword(s):

Transcriptional Activation ◽

Protein Trafficking ◽

Steroid Receptors ◽

Transcriptional Regulatory ◽

Ubiquitin Proteasome ◽

Proteasome Pathway ◽

Receptor Action ◽

Binding Cleft ◽

Hsp 90

Unliganded steroid receptors are assembled into heterocomplexes with heat-shock protein (hsp) 90 by a multiprotein chaperone machinery. In addition to binding the receptors at the chaperone site, hsp90 binds cofactors at other sites that are part of the assembly machinery, as well as immunophilins that connect the assembled receptor-hsp90 heterocomplexes to a protein trafficking pathway. The hsp90-/hsp70-based chaperone machinery interacts with the unliganded glucocorticoid receptor to open the steroid-binding cleft to access by a steroid, and the machinery interacts in very dynamic fashion with the liganded, transformed receptor to facilitate its translocation along microtubular highways to the nucleus. In the nucleus, the chaperone machinery interacts with the receptor in transcriptional regulatory complexes after hormone dissociation to release the receptor and terminate transcriptional activation. By forming heterocomplexes with hsp90, the chaperone machinery stabilizes the receptor to degradation by the ubiquitin-proteasome pathway of proteolysis.

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