Structural basis for distinct roles of SMAD2 and SMAD3 in FOXH1 pioneer-directed TGF-β signaling

Aragón, Eric; Wang, Qiong; Zou, Yilong; Morgani, Sophie M.; Ruiz, Lı́dia; Kaczmarska, Zuzanna; Su, Jie; Torner, Carles; Tian, Lin; Hu, Jing; Shu, Weiqun; Agrawal, Saloni; Gomes, Tiago; Márquez, José Antonio; Hadjantonakis, Anna‐Katerina; Macias, María J.; Massagué, Joan

doi:10.1101/gad.330837.119

Cited by 77 publications

(108 citation statements)

References 65 publications

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“…The new code is applied to evaluate transcription regulatory elements, which have known DNA nucleotide complementary base pairs. For example, an enhancer box or E-box [14] has been correlated to gene expression in neurons, muscles, and other tissues. The DNA base sequence for the E-box is generally considered to be CACGTG.…”

Section: E-boxmentioning

confidence: 99%

New Code for DNA Nucleotide Sequences

Schaper

2020

Preprint

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DNA nucleotides consist of the complementary base pairs of Adenine-Thymine (A-T) and Cytosine-Guanine (C-G) that encode as a sequence for genes, and encode for an upstream initiation site that enables transcription. Recently, this lab has shown that steroid hormones are structurally symmetric with each of the four DNA nucleotide pairs and through an ionic binding process may enable gene transcription. Here, a new code is developed for DNA nucleotide sequences that relates to the initiation site for gene transcription. The structural code consists of the orientation of steroid molecules in binding to DNA nucleotides and the class of steroid molecules that form an intermolecular hydrogen bond with an available functional group of Thymine. This later class thereby describes a steroid hormone-DNA nucleotide-ion complex with three hydrogen bonds for A-T and T-A, which thereby matches the three internal hydrogen bonds associated with C-G and G-C. The code consists of two binary vectors to characterize the four configurations of DNA nucleotides and is shown to be consistent with known regulatory elements of DNA sequences associated with gene transcription, including the TATA box and the E-Box, along with other promoters. In addition, the code, which is bijective, is applied to analyze the DNA sequence associated with SARS-CoV-2 to identify regions with relevant structural characteristics.

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Section: E-boxmentioning

confidence: 99%

New Code for DNA Nucleotide Sequences

Schaper

2020

Preprint

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“…Actually, the DNA-binding capacity of SMAD2 depends on the conformation adopted by the E3 insert ( Figure 5). An open conformation allows SMAD2 to contact DNA while a closed one hinders the β-hairpin structure from interacting with the DNA [154]. Interestingly, it was recently described that this intrinsic structural difference between the two proteins, plays also a role in their subcellular distribution as SMAD3 appears to be mostly nuclear in the absence of ligand while SMAD2 is cytoplasmic and thus becomes more efficiently activated upon TGF-β stimulation [155].…”

Section: Smads In Transcriptionmentioning

confidence: 99%

TGF-β Signaling

2020

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Transforming growth factor-β (TGF-β) represents an evolutionarily conserved family of secreted polypeptide factors that regulate many aspects of physiological embryogenesis and adult tissue homeostasis. The TGF-β family members are also involved in pathophysiological mechanisms that underlie many diseases. Although the family comprises many factors, which exhibit cell type-specific and developmental stage-dependent biological actions, they all signal via conserved signaling pathways. The signaling mechanisms of the TGF-β family are controlled at the extracellular level, where ligand secretion, deposition to the extracellular matrix and activation prior to signaling play important roles. At the plasma membrane level, TGF-βs associate with receptor kinases that mediate phosphorylation-dependent signaling to downstream mediators, mainly the SMAD proteins, and mediate oligomerization-dependent signaling to ubiquitin ligases and intracellular protein kinases. The interplay between SMADs and other signaling proteins mediate regulatory signals that control expression of target genes, RNA processing at multiple levels, mRNA translation and nuclear or cytoplasmic protein regulation. This article emphasizes signaling mechanisms and the importance of biochemical control in executing biological functions by the prototype member of the family, TGF-β.

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“…All clones were confirmed by DNA sequencing. All protein constructs were expressed in E. coli BL21 (DE3) Rosetta following standard procedures as previously described (22)(23)(24). Unlabeled samples were prepared using Luria Broth (LB) (Melford) and minimal media M9 with 15 NH4Cl and/or D- Purified proteins were verified by Liquid chromatography-Mass Spectrometry (LC-MS) using an ACQUITY UPLC Binary Sol MGR LC system (Waters) equipped with a BioSuite Phenyl 1000Å column (Waters, 10 μm RPC 2.0x75 mm) at a flow rate of 100 µL/min.…”

Section: Protein Expression and Purificationmentioning

confidence: 99%

Structures of the germline-specific Deadhead and Thioredoxin T proteins fromDrosophila melanogasterreveal unique features among Thioredoxins

Freier

Aragón

Bagiński

et al. 2020

Preprint

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Thioredoxins (Trxs) are ubiquitous enzymes that regulate the redox state in cells. In Drosophila, there are two germline-specific Trxs, Deadhead (Dhd) and TrxT. Both proteins belong to the L(3)mbt malignant brain tumor signature and to the MMS survival network of genes that mediate the cellular response to DNA damage. Dhd is a maternal protein required for early embryogenesis that promotes protamine-histone exchange in fertilized eggs and midblastula transition. TrxT is testis-specific and associates with the lampbrush loops of the Y chromosome.Here we present the first structures of Dhd and TrxT that unveil new features of these Thioredoxins. Dhd is highly positively charged, unusual in canonical Trxs. This positively charged surface can facilitate its approximation to DNA and to protamine oligomers, to promote chromatin remodeling. On the other hand, TrxT contains a C-terminal extension, mostly unstructured and highly flexible, which wraps the conserved core through a closed conformation. This extension partially covers the catalytic site and modulates the redox activity of the protein.The information provided by these structures can guide future work aimed at understanding how redox inputs modulate the initial steps of embryo development in Drosophila and may help in the design of molecular inhibitors through a structure-based approach.HighlightsWe have determined the first structures of the germline-specific Trxs Dhd and TrxT.Dhd has a highly positively charged surface that facilitates its approximation to DNA and protamine oligomers, to promote chromatin remodeling.TrxT contains a C-terminal extension, highly unusual in canonical Trxs, mostly unstructured and highly flexible.The TrxT C-terminal extension partially covers the catalytic site and modulates the redox activity of the protein.The differences observed in Thioredoxins can help in fine-tuning specific molecules to be active against selected insect species.

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Structural basis for distinct roles of SMAD2 and SMAD3 in FOXH1 pioneer-directed TGF-β signaling

Cited by 77 publications

References 65 publications

New Code for DNA Nucleotide Sequences

New Code for DNA Nucleotide Sequences

TGF-β Signaling

Structures of the germline-specific Deadhead and Thioredoxin T proteins fromDrosophila melanogasterreveal unique features among Thioredoxins

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