scholarly journals Selective cadmium regulation mediated by a cooperative binding mechanism in CadR

2019 ◽  
Vol 116 (41) ◽  
pp. 20398-20403 ◽  
Author(s):  
Xichun Liu ◽  
Qingyuan Hu ◽  
Jinmei Yang ◽  
Shanqing Huang ◽  
Tianbiao Wei ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Spectroscopic Studies ◽  
Cooperative Binding ◽  
Binding Mechanism ◽  
Cadmium Ion ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Optimal Conformation ◽  
Living Organisms ◽  
Insight Into

Detoxification of the highly toxic cadmium element is essential for the survival of living organisms. Pseudomonas putida CadR, a MerR family transcriptional regulator, has been reported to exhibit an ultraspecific response to the cadmium ion. Our crystallographic and spectroscopic studies reveal that the extra cadmium selectivity of CadR is mediated by the unexpected cooperation of thiolate-rich site I and histidine-rich site II. Cadmium binding in site I mediates the reorientation of protein domains and facilitates the assembly of site II. Subsequently, site II bridge-links 2 DNA binding domains through ligands His140/His145 in the C-terminal histidine-rich tail. With dynamic transit between 2 conformational states, this bridge could stabilize the regulator into an optimal conformation that is critical for enhancing the transcriptional activity of the cadmium detoxification system. Our results provide dynamic insight into how nature utilizes the unique cooperative binding mechanism in multisite proteins to recognize cadmium ions specifically.

scholarly journals Protein Kinase A Signaling Pathway Regulates Transcriptional Activity of SAF-1 by Unmasking Its DNA-binding Domains

2003 ◽  
Vol 278 (25) ◽  
pp. 22586-22595 ◽  
Author(s):  
Alpana Ray ◽  
Papiya Ray ◽  
Nicole Guthrie ◽  
Arvind Shakya ◽  
Deepak Kumar ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Dna Binding ◽  
Protein Kinase A ◽  
Signaling Pathway ◽  
Transcriptional Activity ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Kinase A

scholarly journals Orphan nuclear receptor TR3/Nur77 regulates VEGF-A–induced angiogenesis through its transcriptional activity

2006 ◽  
Vol 203 (3) ◽  
pp. 719-729 ◽  
Author(s):  
Huiyan Zeng ◽  
Liuliang Qin ◽  
Dezheng Zhao ◽  
Xiaolian Tan ◽  
Eleanor J. Manseau ◽  
...  
Keyword(s):  
Nuclear Receptor ◽  
Transcriptional Activity ◽  
Umbilical Vein ◽  
Early Response ◽  
Tube Formation ◽  
Orphan Nuclear Receptor ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Umbilical Vein Endothelial Cells

Vascular endothelial growth factor (VEGF)-A has essential roles in vasculogenesis and angiogenesis, but the downstream steps and mechanisms by which human VEGF-A acts are incompletely understood. We report here that human VEGF-A exerts much of its angiogenic activity by up-regulating the expression of TR3 (mouse homologue Nur77), an immediate-early response gene and orphan nuclear receptor transcription factor previously implicated in tumor cell, lymphocyte, and neuronal growth and apoptosis. Overexpression of TR3 in human umbilical vein endothelial cells (HUVECs) resulted in VEGF-A–independent proliferation, survival, and induction of several cell cycle genes, whereas expression of antisense TR3 abrogated the response to VEGF-A in these assays and also inhibited tube formation. Nur77 was highly expressed in several types of VEGF-A–dependent pathological angiogenesis in vivo. Also, using a novel endothelial cell-selective retroviral targeting system, overexpression of Nur77 DNA potently induced angiogenesis in the absence of exogenous VEGF-A, whereas Nur77 antisense strongly inhibited VEGF-A–induced angiogenesis. B16F1 melanoma growth and angiogenesis were greatly inhibited in Nur77−/− mice. Mechanistic studies with TR3/Nur77 mutants revealed that TR3/Nur77 exerted most of its effects on cultured HUVECs and its pro-angiogenic effects in vivo, through its transactivation and DNA binding domains (i.e., through transcriptional activity).

scholarly journals Transcription factor allosteric regulation through substrate coordination to zinc

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Beatriz C Almeida ◽  
Jennifer A Kaczmarek ◽  
Pedro R Figueiredo ◽  
Kristala L J Prather ◽  
Alexandra T P Carvalho
Keyword(s):  
Dna Binding ◽  
Systems Engineering ◽  
Site Directed Mutagenesis ◽  
Structural Isomer ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Zinc Coordination ◽  
Dynamics Simulations ◽  
Insight Into ◽  
Positive Character

Abstract The development of new synthetic biology circuits for biotechnology and medicine requires deeper mechanistic insight into allosteric transcription factors (aTFs). Here we studied the aTF UxuR, a homodimer of two domains connected by a highly flexible linker region. To explore how ligand binding to UxuR affects protein dynamics we performed molecular dynamics simulations in the free protein, the aTF bound to the inducer D-fructuronate or the structural isomer D-glucuronate. We then validated our results by constructing a sensor plasmid for D-fructuronate in Escherichia coli and performed site-directed mutagenesis. Our results show that zinc coordination is necessary for UxuR function since mutation to alanines prevents expression de-repression by D-fructuronate. Analyzing the different complexes, we found that the disordered linker regions allow the N-terminal domains to display fast and large movements. When the inducer is bound, UxuR can sample an open conformation with a more pronounced negative charge at the surface of the N-terminal DNA binding domains. In opposition, in the free and D-glucuronate bond forms the protein samples closed conformations, with a more positive character at the surface of the DNA binding regions. These molecular insights provide a new basis to harness these systems for biological systems engineering.

scholarly journals Structural insight into the specificity of the B3 DNA-binding domains provided by the co-crystal structure of the C-terminal fragment of BfiI restriction enzyme

2014 ◽  
Vol 42 (6) ◽  
pp. 4113-4122 ◽  
Author(s):  
Dmitrij Golovenko ◽  
Elena Manakova ◽  
Linas Zakrys ◽  
Mindaugas Zaremba ◽  
Giedrius Sasnauskas ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Restriction Enzyme ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Terminal Fragment ◽  
Structural Insight ◽  
Insight Into

scholarly journals Association between Hepatocyte Nuclear Factor 6 (HNF-6) and FoxA2 DNA Binding Domains Stimulates FoxA2 Transcriptional Activity but Inhibits HNF-6 DNA Binding

2003 ◽  
Vol 23 (2) ◽  
pp. 437-449 ◽  
Author(s):  
Francisco M. Rausa ◽  
Yongjun Tan ◽  
Robert H. Costa
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Transcriptional Activation ◽  
Transcriptional Activity ◽  
Nuclear Factor ◽  
Hepatocyte Nuclear Factor ◽  
Binding Assays ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Coactivator Protein

ABSTRACT In previous studies we used transgenic mice or recombinant adenovirus infection to increase hepatic expression of forkhead box A2 (FoxA2, previously called hepatocyte nuclear factor 3β [HNF-3β]), which caused diminished hepatocyte glycogen levels and reduced expression of glucose homeostasis genes. Because this diminished expression of FoxA2 target genes was associated with reduced levels of the Cut-Homeodomain HNF-6 transcription factor, we conducted the present study to determine whether there is a functional interaction between HNF-6 and FoxA2. Human hepatoma (HepG2) cotransfection assays demonstrated that HNF-6 synergistically stimulated FoxA2 but not FoxA1 or FoxA3 transcriptional activity, and protein-binding assays showed that this protein interaction required the HNF-6 Cut-Homeodomain and FoxA2 winged-helix DNA binding domains. Furthermore, we show that the HNF-6 Cut-Homeodomain sequences were sufficient to synergistically stimulate FoxA2 transcriptional activation by recruiting the p300/CBP coactivator proteins. This was supported by the fact that FoxA2 transcriptional synergy with HNF-6 was dependent on retention of the HNF-6 Cut domain LXXLL sequence, which mediated recruitment of the p300/CBP proteins. Moreover, cotransfection and DNA binding assays demonstrated that increased FoxA2 levels caused a decrease in HNF-6 transcriptional activation of the glucose transporter 2 (Glut-2) promoter by interfering with the binding of HNF-6 to its target DNA sequence. These data suggest that at a FoxA-specific site, HNF-6 serves as a coactivator protein to enhance FoxA2 transcription, whereas at an HNF-6-specific site, FoxA2 represses HNF-6 transcription by inhibiting HNF-6 DNA binding activity. This is the first reported example of a liver-enriched transcription factor (HNF-6) functioning as a coactivator protein to potentiate the transcriptional activity of another liver factor, FoxA2.

scholarly journals Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Sharon A. Huws ◽  
Joan E. Edwards ◽  
Wanchang Lin ◽  
Francesco Rubino ◽  
Mark Alston ◽  
...  
Keyword(s):  
Energy Harvesting ◽  
Perennial Ryegrass ◽  
Transcriptional Activity ◽  
Ecological Niches ◽  
Ecological Interactions ◽  
Carbohydrate Degradation ◽  
Host Nutrition ◽  
Role Based ◽  
Insight Into

Abstract Background Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions facilitating energy harvesting at the fresh perennial ryegrass (PRG)-biofilm interface in the rumen using an in sacco approach and prokaryotic metatranscriptomic profiling. Results Network analysis identified two distinct sub-microbiomes primarily representing primary (≤ 4 h) and secondary (≥ 4 h) colonisation phases and the most transcriptionally active bacterial families (i.e Fibrobacteriaceae, Selemondaceae and Methanobacteriaceae) did not interact with either sub-microbiome, indicating non-cooperative behaviour. Conversely, Prevotellaceae had most transcriptional activity within the primary sub-microbiome (focussed on protein metabolism) and Lachnospiraceae within the secondary sub-microbiome (focussed on carbohydrate degradation). Putative keystone taxa, with low transcriptional activity, were identified within both sub-microbiomes, highlighting the important synergistic role of minor bacterial families; however, we hypothesise that they may be ‘cheating’ in order to capitalise on the energy-harvesting capacity of other microbes. In terms of chemical cues underlying transition from primary to secondary colonisation phases, we suggest that AI-2-based quorum sensing plays a role, based on LuxS gene expression data, coupled with changes in PRG chemistry. Conclusions In summary, we show that fresh PRG-attached prokaryotes are resilient and adapt quickly to changing niches. This study provides the first major insight into the complex temporal ecological interactions occurring at the plant-biofilm interface within the rumen. The study also provides valuable insights into potential plant breeding strategies for development of the utopian plant, allowing optimal sustainable production of ruminants.

scholarly journals The apple C2H2-type zinc finger transcription factor MdZAT10 positively regulates JA-induced leaf senescence by interacting with MdBT2

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Kuo Yang ◽  
Jian-Ping An ◽  
Chong-Yang Li ◽  
Xue-Na Shen ◽  
Ya-Jing Liu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Transcription Factor ◽  
Liquid Chromatography ◽  
Zinc Finger ◽  
Leaf Senescence ◽  
Transcriptional Activity ◽  
Molecular Mechanisms ◽  
Liquid Chromatography Mass Spectrometry ◽  
Zinc Finger Transcription Factor ◽  
Insight Into

AbstractJasmonic acid (JA) plays an important role in regulating leaf senescence. However, the molecular mechanisms of leaf senescence in apple (Malus domestica) remain elusive. In this study, we found that MdZAT10, a C2H2-type zinc finger transcription factor (TF) in apple, markedly accelerates leaf senescence and increases the expression of senescence-related genes. To explore how MdZAT10 promotes leaf senescence, we carried out liquid chromatography/mass spectrometry screening. We found that MdABI5 physically interacts with MdZAT10. MdABI5, an important positive regulator of leaf senescence, significantly accelerated leaf senescence in apple. MdZAT10 was found to enhance the transcriptional activity of MdABI5 for MdNYC1 and MdNYE1, thus accelerating leaf senescence. In addition, we found that MdZAT10 expression was induced by methyl jasmonate (MeJA), which accelerated JA-induced leaf senescence. We also found that the JA-responsive protein MdBT2 directly interacts with MdZAT10 and reduces its protein stability through ubiquitination and degradation, thereby delaying MdZAT10-mediated leaf senescence. Taken together, our results provide new insight into the mechanisms by which MdZAT10 positively regulates JA-induced leaf senescence in apple.

scholarly journals R Coronae Borealis Stars: Long-Term Photometric & Spectroscopic Studies

1998 ◽  
Vol 11 (1) ◽  
pp. 379-379
Author(s):  
P.L. Cottrell ◽  
L. Skuljan ◽  
P.M. Kilmartin ◽  
C. Gilmore ◽  
W.A. Lawson
Keyword(s):  
Radial Velocity ◽  
Spectroscopic Studies ◽  
Photometric Data ◽  
Decline Phase ◽  
Dust Clouds ◽  
Medium Resolution ◽  
Formation And Evolution ◽  
R Coronae Borealis Stars ◽  
Insight Into

For more than a decade we have been able to acquire and analyse a significant amount of photometric data of the highly variable R Coronae Borealis (RCB) stars. This has made been possible by a photometric service observing programme instigated at the Observatory. These photometric data have been combined with less extensive spectroscopic coverage, particularly of the decline phase of these stars. These have been supplemented by observations obtained at Mount Stromlo and Siding Spring Observatories for a radial velocity study. Significantly more spectroscopic observations are now being acquired with the development of a new medium resolution spectrograph at Mount John University Observatory. In this poster we will present recent photometric and spectroscopic results for a number of the RCB stars in our sample. This observational and analysis work can be used to provide further insight into the nature of these stars, their likely progeny and progenitors and the processes that are involved in the formation and evolution of the obscuring dust clouds which cause the decline phase.

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