Mechanisms of transcriptional regulation by WT1 (Wilms’ tumour 1)

The WT1 (Wilms’ tumour 1) gene encodes a zinc finger transcription factor and RNA-binding protein that direct the development of several organs and tissues. WT1 manifests both tumour suppressor and oncogenic activities, but the reasons behind these opposing functions are still not clear. As a transcriptional regulator, WT1 can either activate or repress numerous target genes resulting in disparate biological effects such as growth, differentiation and apoptosis. The complex nature of WT1 is exemplified by a plethora of isoforms, post-translational modifications and multiple binding partners. How WT1 achieves specificity to regulate a large number of target genes involved in diverse physiological processes is the focus of the present review. We discuss the wealth of the growing molecular information that defines our current understanding of the versatility and utility of WT1 as a master regulator of organ development, a tumour suppressor and an oncogene.

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Protein and Proteome Atlas for Plants under Stresses: New Highlights and Ways for Integrated Omics in Post-Genomics Era

International Journal of Molecular Sciences ◽

10.3390/ijms20205222 ◽

2019 ◽

Vol 20 (20) ◽

pp. 5222 ◽

Cited By ~ 3

Author(s):

Xuchu Wang

Keyword(s):

Protein Identification ◽

Target Genes ◽

Protein Quantification ◽

Plant Proteins ◽

Post Translational Modifications ◽

Physiological Processes ◽

Integrated Omics ◽

Response To Stress ◽

And Function ◽

Integrative Omics

In the post-genomics era, integrative omics studies for biochemical, physiological, and molecular changes of plants in response to stress conditions play more crucial roles. Among them, atlas analysis of plants under different abiotic stresses, including salinity, drought, and toxic conditions, has become more important for uncovering the potential key genes and proteins in different plant tissues. High-quality genomic data and integrated analyses of transcriptomic, proteomic, metabolomics, and phenomic patterns provide a deeper understanding of how plants grow and survive under environmental stresses. This editorial mini-review aims to synthesize the 27 papers including two timely reviews that have contributed to this Special Issue, which focuses on concluding the recent progress in the Protein and Proteome Atlas in plants under different stresses. It covers various aspects of plant proteins ranging from agricultural proteomics, structure and function of proteins, novel techniques and approaches for gene and protein identification, protein quantification, proteomics for post-translational modifications (PTMs), and new insights into proteomics. The proteomics-based results in this issue will help the readers to gain novel insights for the understanding of complicated physiological processes in crops and other important plants in response to stressed conditions. Furthermore, these target genes and proteins that are important candidates for further functional validation in economic plants and crops can be studied.

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MicroRNA Member TaMIR5062 in T. Aestivum Involves Plant Drought and Salt Acclimation via Regulating Physiological Processes Associated with Water Retention and ROS Homeostasis

10.21203/rs.3.rs-1137207/v1 ◽

2021 ◽

Author(s):

Yuanjinzi Qiao ◽

Ling Wang ◽

Zidi Yu ◽

Chenyang Ni ◽

Tianjiao Li ◽

...

Keyword(s):

Water Retention ◽

Target Genes ◽

Rna Binding ◽

Growth Traits ◽

Critical Role ◽

Mirna Regulation ◽

Physiological Processes ◽

Ros Homeostasis ◽

Drought And Salt Tolerance ◽

Growth Features

Abstract microRNA members negatively regulate target genes via posttranscriptional cleavage or translation repression mechanisms, impacting on plant growth, development, and stress response. In this study, we characterized TaMIR5062, a miRNA member in T. aestivum, in mediating drought and salt responses. TaMIR5062 interacts with six target genes, including two encoding calmodulins, three coding for 4-oxalocrotonate tautomerases, and one for pumilio-family RNA binding domain protein. The TaMIR5062 transcripts were gradually upregulated in plants upon 27-h drought and salt treatments, whose induced expression under stress treatments was restored following the normal recovery condition. Tobacco (N. tabacum) lines transformed with TaMIR5062 modified growth traits under drought and salt treatments; the lines overexpressing miRNA (i.e., Sen 1 and Sen 2) improved growth traits (i.e., biomass, leaf area, and root length) whereas those with knockdown (Anti 1) alleviated growth features compared with wild type. These results suggested the critical role of TaMIR5062 in improving plant drought and salt tolerance. In line with growth traits in stress-challenged lines, improved leaf water retention (i.e., promoted stomata closing, water losing rate, and osmolytes) and ROS-associated parameters (higher SOD, CAT, and POD activities, etc.) were shown in Sen 1 and Sen 2 under stress conditions. Antioxidant enzyme (AE) genes NtMnSOD1, NtCAT, and NtPOD9 encoding SOD, CAT, and POD, respectively, enhanced transcription in Sen 1 and downregulated expression in Anti 1 challenged with drought and salt stress. These results suggested the improved ROS homeostasis mediated by TaMIR5062 associates modified expression of distinct AE genes. Quantities of genes functional into categories “biological process”, “cellular component”, and “molecular function” contribute to TaMIR5062-mediated osmotic stress adaptation by regulating distinct biological pathways (i.e., protein folding) and metabolisms (i.e., photosynthesis and isoprenoid biosynthesis), which impact on plant osmotic-regulation, ROS homeostasis, and stress defensiveness underlying miRNA regulation. TaMIR5062 is a valuable target for molecular breeding of drought-tolerant crop cultivars.

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TARGET GENES OF THE WILMS' TUMOUR SUPPRESSOR GENE AS IDENTIFIED BY cDNA EXPRESSION PROFILING

Nephrology ◽

10.1046/j.1440-1797.2002.00007-1-5.x ◽

2002 ◽

Vol 7 (1) ◽

pp. A5-A5

Author(s):

Little M.H ◽

Forrest A ◽

Grimmond S ◽

Lindsay M ◽

Martinez G ◽

...

Keyword(s):

Expression Profiling ◽

Target Genes ◽

Suppressor Gene ◽

Tumour Suppressor Gene ◽

Tumour Suppressor ◽

Wilms Tumour ◽

Cdna Expression

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MiR-193a-3p is an Important Tumour Suppressor in Lung Cancer and Directly Targets KRAS

Cellular Physiology and Biochemistry ◽

10.1159/000485491 ◽

2017 ◽

Vol 44 (4) ◽

pp. 1311-1324 ◽

Cited By ~ 21

Author(s):

Qian Fan ◽

Xiuting Hu ◽

Haiyang Zhang ◽

Shengguang Wang ◽

Huilai Zhang ◽

...

Keyword(s):

Lung Cancer ◽

Cell Migration ◽

Target Genes ◽

Biological Effects ◽

Tumour Suppressor ◽

Luciferase Reporter ◽

Cellular Functions ◽

Reporter Assays

Background/Aims: MicroRNAs (miRNAs) have emerged as major regulators of tumour development and progression in non-small cell lung cancer (NSCLC). However, the role of miR-193a-3p in NSCLC is still unclear. Methods: Quantitative RT-PCR was used to detect miR-193a-3p expression levels in NSCLC tumour tissues. CCK8, EdU and cell migration assays were performed to analyse the biological functions of miR-193a-3p in NSCLC cells. Luciferase reporter assays were used to validate the bioinformatics-predicted target genes of miR-193a-3p. Western blotting and RNA/DNA interference carried out to evaluate the association between miR-193a-3p and KRAS. Results: miR-193a-3p expression was decreased in the NSCLC tumour tissues. We investigated the biological effects of miR-193a-3p both in vivo and in vitro and found that enforced expression of miR-193a-3p inhibited tumour formation and suppressed cell proliferation and cell migration. KRAS was found to be a potential target of miR-193a-3p, and dual luciferase reporter assays showed that miR-193a-3p directly binds to the 3’-untranslated region (3’-UTR) of KRAS mRNA. In addition, we found that changing the expression of KRAS had the opposite results to those induced by miR-193a-3p in the NSCLC cells. Importantly, simultaneous overexpression of miR-193a-3p and KRAS could counteract the effects of both on cellular functions. Conclusion: These findings highlight an important role for miR-193a-3p as a tumour suppressor in NSCLC pathogenesis via the regulation of KRAS expression.

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Reading the phosphorylation code: binding of the 14-3-3 protein to multivalent client phosphoproteins

Biochemical Journal ◽

10.1042/bcj20200084 ◽

2020 ◽

Vol 477 (7) ◽

pp. 1219-1225 ◽

Cited By ~ 4

Author(s):

Nikolai N. Sluchanko

Keyword(s):

Protein Function ◽

Intrinsically Disordered Protein ◽

Structural Basis ◽

Major Protein ◽

Post Translational Modifications ◽

Protein Protein Interaction ◽

Intrinsically Disordered ◽

Biochemical Journal ◽

Multiple Binding ◽

And Control

Many major protein–protein interaction networks are maintained by ‘hub’ proteins with multiple binding partners, where interactions are often facilitated by intrinsically disordered protein regions that undergo post-translational modifications, such as phosphorylation. Phosphorylation can directly affect protein function and control recognition by proteins that ‘read’ the phosphorylation code, re-wiring the interactome. The eukaryotic 14-3-3 proteins recognizing multiple phosphoproteins nicely exemplify these concepts. Although recent studies established the biochemical and structural basis for the interaction of the 14-3-3 dimers with several phosphorylated clients, understanding their assembly with partners phosphorylated at multiple sites represents a challenge. Suboptimal sequence context around the phosphorylated residue may reduce binding affinity, resulting in quantitative differences for distinct phosphorylation sites, making hierarchy and priority in their binding rather uncertain. Recently, Stevers et al. [Biochemical Journal (2017) 474: 1273–1287] undertook a remarkable attempt to untangle the mechanism of 14-3-3 dimer binding to leucine-rich repeat kinase 2 (LRRK2) that contains multiple candidate 14-3-3-binding sites and is mutated in Parkinson's disease. By using the protein-peptide binding approach, the authors systematically analyzed affinities for a set of LRRK2 phosphopeptides, alone or in combination, to a 14-3-3 protein and determined crystal structures for 14-3-3 complexes with selected phosphopeptides. This study addresses a long-standing question in the 14-3-3 biology, unearthing a range of important details that are relevant for understanding binding mechanisms of other polyvalent proteins.

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Molecular Dynamics of Cobalt Protoporphyrin Antagonism of the Cancer Suppressor REV-ERBβ

Molecules ◽

10.3390/molecules26113251 ◽

2021 ◽

Vol 26 (11) ◽

pp. 3251

Author(s):

Taufik Muhammad Fakih ◽

Fransiska Kurniawan ◽

Muhammad Yusuf ◽

Mudasir Mudasir ◽

Daryono Hadi Tjahjono

Keyword(s):

Binding Site ◽

Nuclear Receptor ◽

Target Genes ◽

Protoporphyrin Ix ◽

Binding Energies ◽

Metal Center ◽

Complex Nature ◽

Dynamic Simulations ◽

Subtle Change ◽

Cobalt Protoporphyrin

Nuclear receptor REV-ERBβ is an overexpressed oncoprotein that has been used as a target for cancer treatment. The metal-complex nature of its ligand, iron protoporphyrin IX (Heme), enables the REV-ERBβ to be used for multiple therapeutic modalities as a photonuclease, a photosensitizer, or a fluorescence imaging agent. The replacement of iron with cobalt as the metal center of protoporphyrin IX changes the ligand from an agonist to an antagonist of REV-ERBβ. The mechanism behind that phenomenon is still unclear, despite the availability of crystal structures of REV-ERBβ in complex with Heme and cobalt protoporphyrin IX (CoPP). This study used molecular dynamic simulations to compare the effects of REV-ERBβ binding to Heme and CoPP, respectively. The initial poses of Heme and CoPP in complex with agonist and antagonist forms of REV-ERBβ were predicted using molecular docking. The binding energies of each ligand were calculated using the MM/PBSA method. The computed binding affinity of Heme to REV-ERBβ was stronger than that of CoPP, in agreement with experimental results. CoPP altered the conformation of the ligand-binding site of REV-ERBβ, disrupting the binding site for nuclear receptor corepressor, which is required for REV-ERBβ to regulate the transcription of downstream target genes. Those results suggest that a subtle change in the metal center of porphyrin can change the behavior of porphyrin in cancer cell signaling. Therefore, modification of porphyrin-based agents for cancer therapy should be conducted carefully to avoid triggering unfavorable effects.

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Histone deacetylase (HDAC) 9: versatile biological functions and emerging roles in human cancer

Cellular Oncology ◽

10.1007/s13402-021-00626-9 ◽

2021 ◽

Author(s):

Chun Yang ◽

Stéphane Croteau ◽

Pierre Hardy

Keyword(s):

Histone Deacetylase ◽

Posttranslational Modifications ◽

Histone Deacetylases ◽

Muscle Development ◽

Target Genes ◽

Human Cancer ◽

Expression Patterns ◽

Aberrant Expression ◽

Physiological Processes ◽

Cancer Pathogenesis

Abstract Background HDAC9 (histone deacetylase 9) belongs to the class IIa family of histone deacetylases. This enzyme can shuttle freely between the nucleus and cytoplasm and promotes tissue-specific transcriptional regulation by interacting with histone and non-histone substrates. HDAC9 plays an essential role in diverse physiological processes including cardiac muscle development, bone formation, adipocyte differentiation and innate immunity. HDAC9 inhibition or activation is therefore a promising avenue for therapeutic intervention in several diseases. HDAC9 overexpression is also common in cancer cells, where HDAC9 alters the expression and activity of numerous relevant proteins involved in carcinogenesis. Conclusions This review summarizes the most recent discoveries regarding HDAC9 as a crucial regulator of specific physiological systems and, more importantly, highlights the diverse spectrum of HDAC9-mediated posttranslational modifications and their contributions to cancer pathogenesis. HDAC9 is a potential novel therapeutic target, and the restoration of aberrant expression patterns observed among HDAC9 target genes and their related signaling pathways may provide opportunities to the design of novel anticancer therapeutic strategies.

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Cryo-EM structure of human Wntless in complex with Wnt3a

Nature Communications ◽

10.1038/s41467-021-24731-3 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Qing Zhong ◽

Yanyu Zhao ◽

Fangfei Ye ◽

Zaiyu Xiao ◽

Gaoxingyu Huang ◽

...

Keyword(s):

Transmembrane Domain ◽

Transmembrane Protein ◽

Multiple Interfaces ◽

Wnt Proteins ◽

Binding Partners ◽

Multiple Binding Sites ◽

Evolutionarily Conserved ◽

Multiple Binding ◽

Hydrophobic Tunnel ◽

Conserved Core

AbstractWntless (WLS), an evolutionarily conserved multi-pass transmembrane protein, is essential for secretion of Wnt proteins. Wnt-triggered signaling pathways control many crucial life events, whereas aberrant Wnt signaling is tightly associated with many human diseases including cancers. Here, we report the cryo-EM structure of human WLS in complex with Wnt3a, the most widely studied Wnt, at 2.2 Å resolution. The transmembrane domain of WLS bears a GPCR fold, with a conserved core cavity and a lateral opening. Wnt3a interacts with WLS at multiple interfaces, with the lipid moiety on Wnt3a traversing a hydrophobic tunnel of WLS transmembrane domain and inserting into membrane. A β-hairpin of Wnt3a containing the conserved palmitoleoylation site interacts with WLS extensively, which is crucial for WLS-mediated Wnt secretion. The flexibility of the Wnt3a loop/hairpin regions involved in the multiple binding sites indicates induced fit might happen when Wnts are bound to different binding partners. Our findings provide important insights into the molecular mechanism of Wnt palmitoleoylation, secretion and signaling.

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The Combined Human Genotype of Truncating TTN and RBM20 Mutations Is Associated with Severe and Early Onset of Dilated Cardiomyopathy

Genes ◽

10.3390/genes12060883 ◽

2021 ◽

Vol 12 (6) ◽

pp. 883

Author(s):

Anna Gaertner ◽

Julia Bloebaum ◽

Andreas Brodehl ◽

Baerbel Klauke ◽

Katharina Sielemann ◽

...

Keyword(s):

Heart Failure ◽

Dilated Cardiomyopathy ◽

Early Onset ◽

Target Genes ◽

Frameshift Mutation ◽

Rna Binding ◽

Splicing Factor ◽

Binding Motif ◽

Rich Domain ◽

Generation Sequencing

A major cause of heart failure is cardiomyopathies, with dilated cardiomyopathy (DCM) as the most common form. Over 40 genes are linked to DCM, among them TTN and RBM20. Next Generation Sequencing in clinical DCM cohorts revealed truncating variants in TTN (TTNtv), accounting for up to 25% of familial DCM cases. Mutations in the cardiac splicing factor RNA binding motif protein 20 (RBM20) are also known to be associated with severe cardiomyopathies. TTN is one of the major RBM20 splicing targets. Most of the pathogenic RBM20 mutations are localized in the highly conserved arginine serine rich domain (RS), leading to a cytoplasmic mislocalization of mutant RBM20. Here, we present a patient with an early onset DCM carrying a combination of (likely) pathogenic TTN and RBM20 mutations. We show that the splicing of RBM20 target genes is affected in the mutation carrier. Furthermore, we reveal RBM20 haploinsufficiency presumably caused by the frameshift mutation in RBM20.

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The noncoding MIR100HG RNA enhances the autocrine function of transforming growth factor β signaling

Oncogene ◽

10.1038/s41388-021-01803-8 ◽

2021 ◽

Author(s):

Panagiotis Papoutsoglou ◽

Dorival Mendes Rodrigues-Junior ◽

Anita Morén ◽

Andrew Bergman ◽

Fredrik Pontén ◽

...

Keyword(s):

Growth Factor ◽

Target Genes ◽

Rna Binding ◽

Transforming Growth Factor ◽

Transforming Growth Factor Β ◽

Tgfβ Signaling ◽

Ribonucleoprotein Complexes ◽

Expression Of Genes ◽

Downstream Effectors ◽

Human Carcinomas

AbstractActivation of the transforming growth factor β (TGFβ) pathway modulates the expression of genes involved in cell growth arrest, motility, and embryogenesis. An expression screen for long noncoding RNAs indicated that TGFβ induced mir-100-let-7a-2-mir-125b-1 cluster host gene (MIR100HG) expression in diverse cancer types, thus confirming an earlier demonstration of TGFβ-mediated transcriptional induction of MIR100HG in pancreatic adenocarcinoma. MIR100HG depletion attenuated TGFβ signaling, expression of TGFβ-target genes, and TGFβ-mediated cell cycle arrest. Moreover, MIR100HG silencing inhibited both normal and cancer cell motility and enhanced the cytotoxicity of cytostatic drugs. MIR100HG overexpression had an inverse impact on TGFβ signaling responses. Screening for downstream effectors of MIR100HG identified the ligand TGFβ1. MIR100HG and TGFB1 mRNA formed ribonucleoprotein complexes with the RNA-binding protein HuR, promoting TGFβ1 cytokine secretion. In addition, TGFβ regulated let-7a-2–3p, miR-125b-5p, and miR-125b-1–3p expression, all encoded by MIR100HG intron-3. Certain intron-3 miRNAs may be involved in TGFβ/SMAD-mediated responses (let-7a-2–3p) and others (miR-100, miR-125b) in resistance to cytotoxic drugs mediated by MIR100HG. In support of a model whereby TGFβ induces MIR100HG, which then enhances TGFβ1 secretion, analysis of human carcinomas showed that MIR100HG expression correlated with expression of TGFB1 and its downstream extracellular target TGFBI. Thus, MIR100HG controls the magnitude of TGFβ signaling via TGFβ1 autoinduction and secretion in carcinomas.

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