Correction: Transcriptional factors Smad1 and Smad9 act redundantly to mediate zebrafish ventral specification downstream of Smad5. [Additions and Corrections]
VOLUME 289 (2014) PAGES 6604–6618In Fig. 4G, in the foxi1 panel, the images in Fig. 4G, i and l, corresponding to “smad1 MO” and “smad5 MO + samd1/9 mRNA” samples, respectively, were inadvertently reused during figure preparation. This error has now been corrected using images pertaining to each treatment and sample. This correction does not affect the results or conclusions of the work.jbc;295/52/18650/F4F1F4Figure 4G. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - December 25, 2020 Category: Chemistry Authors: Chang-Yong Wei, Hou-Peng Wang, Zuo-Yan Zhu, Yong-Hua Sun Tags: Additions and Corrections Source Type: research

Withdrawal: MicroRNA-7 compromises p53-dependent apoptosis by controlling the expression of the chromatin remodeling factor SMARCD1 [Withdrawals/Retractions]
This article has been withdrawn by all the authors. The Journal pointed out that the p53 immunoblot from H1975 in Fig. 3F was reused in Fig. 4E (α-tubulin) and Fig. 5A (p53 from A549), representing different experimental conditions. There are duplicated immunoblots representing different experimental conditions in the last column of Fig. 4B (α-tubulin) and first column of Fig 5E. There is a duplicated FACS plot in Fig. 3G (H1975 scramble) and Fig. 4F (H1975 ctrl). There is a duplicated FACS plot in Fig. 5D (H1975 scramble) and Fig. 5F (ctrl). There are some duplicated immunoblots in Fig. 2A (A549 SMARDC1) and Fig. 4A (SM...
Source: Journal of Biological Chemistry - December 25, 2020 Category: Chemistry Authors: Chun-Fu Hong, Shu-Yu Lin, Yu-Ting Chou, Cheng-Wen Wu Tags: Withdrawals/Retractions Source Type: research

Transcription factor NF-{kappa}B promotes acute lung inȷury via microRNA-99b-mediated PRDM1 down-regulation [Developmental Biology]
Acute lung injury (ALI), is a rapidly progressing heterogenous pulmonary disorder that possesses a high risk of mortality. Accumulating evidence has implicated the activation of the p65 subunit of NF-κB [NF-κB(p65)] activation in the pathological process of ALI. microRNAs (miRNAs), a group of small RNA molecules, have emerged as major governors due to their post-transcriptional regulation of gene expression in a wide array of pathological processes, including ALI. The dysregulation of miRNAs and NF-κB activation has been implicated in human diseases. In the current study, we set out to decipher the convergence of miR-99...
Source: Journal of Biological Chemistry - December 25, 2020 Category: Chemistry Authors: Jie Zhao, Fei Xie, Ruidong Chen, Zhen Zhang, Rujun Dai, Na Zhao, Rongxin Wang, Yanhong Sun, Yue Chen Tags: Cell Biology Source Type: research

Ascertaining the biochemical function of an essential pectin methylesterase in the gut microbe Bacteroides thetaiotaomicron [Metabolism]
Pectins are a major dietary nutrient source for the human gut microbiota. The prominent gut microbe Bacteroides thetaiotaomicron was recently shown to encode the founding member (BT1017) of a new family of pectin methylesterases essential for the metabolism of the complex pectin rhamnogalacturonan-II (RG-II). However, biochemical and structural knowledge of this family is lacking. Here, we showed that BT1017 is critical for the metabolism of an RG-II–derived oligosaccharide ΔBT1017oligoB generated by a BT1017 deletion mutant (ΔBT1017) during growth on carbohydrate extract from apple juice. Structural analyses of ΔBT10...
Source: Journal of Biological Chemistry - December 25, 2020 Category: Chemistry Authors: Cheng–Jie Duan, Arnaud Basle, Marcelo Visona Liberato, Joseph Gray, Sergey A. Nepogodiev, Robert A. Field, Nathalie Juge, Didier Ndeh Tags: Enzymology Source Type: research

Ischemic stroke disrupts the endothelial glycocalyx through activation of proHPSE via acrolein exposure [Molecular Bases of Disease]
In this study, glycosaminoglycans, a component of the endothelial glycocalyx, were studied in the context of ischemic stroke using a photochemically induced thrombosis mouse model. Decreased levels of heparan sulfate and chondroitin sulfate and increased activity of hyaluronidase 1 and heparanase (HPSE) were observed in ischemic brain tissues. HPSE expression in cerebral vessels increased after stroke onset and infarct volume greatly decreased after co-administration of N-acetylcysteine + glycosaminoglycan oligosaccharides as compared with N-acetylcysteine administration alone. These results suggest that the endothelial gl...
Source: Journal of Biological Chemistry - December 25, 2020 Category: Chemistry Authors: Kenta Ko, Takehiro Suzuki, Ryota Ishikawa, Natsuko Hattori, Risako Ito, Kenta Umehara, Tomomi Furihata, Naoshi Dohmae, Robert J. Linhardt, Kazuei Igarashi, Toshihiko Toida, Kyohei Higashi Tags: Glycobiology and Extracellular Matrices Source Type: research

Neuroligin-2 dependent conformational activation of collybistin reconstituted in supported hybrid membranes [Membrane Biology]
The assembly of the postsynaptic transmitter sensing machinery at inhibitory nerve cell synapses requires the intimate interplay between cell adhesion proteins, scaffold and adaptor proteins, and γ-aminobutyric acid (GABA) or glycine receptors. We developed an in vitro membrane system to reconstitute this process, to identify the essential protein components, and to define their mechanism of action, with a specific focus on the mechanism by which the cytosolic C terminus of the synaptic cell adhesion protein Neuroligin-2 alters the conformation of the adaptor protein Collybistin-2 and thereby controls Collybistin-2-intera...
Source: Journal of Biological Chemistry - December 25, 2020 Category: Chemistry Authors: Jonas Schafer, Lucas Forster, Ingo Mey, Theofilos Papadopoulos, Nils Brose, Claudia Steinem Tags: Neurobiology Source Type: research

Molecular architecture and domain arrangement of the placental malaria protein VAR2CSA suggests a model for carbohydrate binding [Glycobiology and Extracellular Matrices]
VAR2CSA is the placental-malaria–specific member of the antigenically variant Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family. It is expressed on the surface of Plasmodium falciparum-infected host red blood cells and binds to specific chondroitin-4-sulfate chains of the placental proteoglycan receptor. The functional ∼310 kDa ectodomain of VAR2CSA is a multidomain protein that requires a minimum 12-mer chondroitin-4-sulfate molecule for specific, high affinity receptor binding. However, it is not known how the individual domains are organized and interact to create the receptor-binding surface, lim...
Source: Journal of Biological Chemistry - December 25, 2020 Category: Chemistry Authors: Maria C. Bewley, Lovely Gautam, Mashanipalya G. Jagadeeshaprasad, D. Channe Gowda, John M. Flanagan Tags: Molecular Biophysics Source Type: research

High affinity binding of SARS-CoV-2 spike protein enhances ACE2 carboxypeptidase activity [Molecular Bases of Disease]
The novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) has emerged to a pandemic and caused global public health crisis. Human angiotensin-converting enzyme 2(ACE2) was identified as the entry receptor for SARS-CoV-2. As a carboxypeptidase, ACE2 cleaves many biological substrates besides angiotensin II to control vasodilatation and vascular permeability. Given the nanomolar high affinity between ACE2 and SARS-CoV-2 spike protein, we investigated how this interaction would affect the enzymatic activity of ACE2. Surprisingly, SARS-CoV-2 trimeric spike protein increased ACE2 proteolytic activity ∼3-10 fold aga...
Source: Journal of Biological Chemistry - December 25, 2020 Category: Chemistry Authors: Jinghua Lu, Peter D. Sun Tags: Enzymology Source Type: research

Conserved biophysical features of the CaV2 presynaptic Ca2+ channel homologue from the early-diverging animal Trichoplax adhaerens [Membrane Biology]
The dominant role of CaV2 voltage-gated calcium channels for driving neurotransmitter release is broadly conserved. Given the overlapping functional properties of CaV2 and CaV1 channels, and less so CaV3 channels, it is unclear why there have not been major shifts toward dependence on other CaV channels for synaptic transmission. Here, we provide a structural and functional profile of the CaV2 channel cloned from the early-diverging animal Trichoplax adhaerens, which lacks a nervous system but possesses single gene homologues for CaV1–CaV3 channels. Remarkably, the highly divergent channel possesses similar features as h...
Source: Journal of Biological Chemistry - December 25, 2020 Category: Chemistry Authors: Julia Gauberg, Salsabil Abdallah, Wassim Elkhatib, Alicia N. Harracksingh, Thomas Piekut, Elise F. Stanley, Adriano Senatore Tags: Molecular Biophysics Source Type: research

Unique active-site and subsite features in the arabinogalactan-degrading GH43 exo-{beta}-1,3-galactanase from Phanerochaete chrysosporium [Enzymology]
In this study, we solved the apo and liganded structures of Pc1,3Gal43A, which reveal a glycoside hydrolase family 43 subfamily 24 (GH43_sub24) catalytic domain together with a carbohydrate-binding module family 35 (CBM35) binding domain. GH43_sub24 is known to lack the catalytic base Asp conserved among other GH43 subfamilies. Our structure in combination with kinetic analyses reveals that the tautomerized imidic acid group of Gln263 serves as the catalytic base residue instead. Pc1,3Gal43A has three subsites that continue from the bottom of the catalytic pocket to the solvent. Subsite −1 contains a space that can accom...
Source: Journal of Biological Chemistry - December 25, 2020 Category: Chemistry Authors: Kaori Matsuyama, Naomi Kishine, Zui Fujimoto, Naoki Sunagawa, Toshihisa Kotake, Yoichi Tsumuraya, Masahiro Samejima, Kiyohiko Igarashi, Satoshi Kaneko Tags: Protein Structure and Folding Source Type: research

Solvent accessibility changes in a Na+-dependent C4-dicarboxylate transporter suggest differential substrate effects in a multistep mechanism [Membrane Biology]
The divalent anion sodium symporter (DASS) family (SLC13) plays critical roles in metabolic homeostasis, influencing many processes, including fatty acid synthesis, insulin resistance, and adiposity. DASS transporters catalyze the Na+-driven concentrative uptake of Krebs cycle intermediates and sulfate into cells; disrupting their function can protect against age-related metabolic diseases and can extend lifespan. An inward-facing crystal structure and an outward-facing model of a bacterial DASS family member, VcINDY from Vibrio cholerae, predict an elevator-like transport mechanism involving a large rigid body movement of...
Source: Journal of Biological Chemistry - December 25, 2020 Category: Chemistry Authors: Connor D. D. Sampson, Matthew J. Stewart, Joseph A. Mindell, Christopher Mulligan Tags: Membrane Biology Source Type: research

Differential compartmental processing and phosphorylation of pathogenic human tau and native mouse tau in the line 66 model of frontotemporal dementia [Molecular Bases of Disease]
Synapse loss is associated with motor and cognitive decline in multiple neurodegenerative disorders, and the cellular redistribution of tau is related to synaptic impairment in tauopathies, such as Alzheimer's disease and frontotemporal dementia. Here, we examined the cellular distribution of tau protein species in human tau overexpressing line 66 mice, a transgenic mouse model akin to genetic variants of frontotemporal dementia. Line 66 mice express intracellular tau aggregates in multiple brain regions and exhibit sensorimotor and motor learning deficiencies. Using a series of anti-tau antibodies, we observed, histologic...
Source: Journal of Biological Chemistry - December 25, 2020 Category: Chemistry Authors: Nora Lemke, Valeria Melis, Dilyara Lauer, Mandy Magbagbeolu, Boris Neumann, Charles R. Harrington, Gernot Riedel, Claude M. Wischik, Franz Theuring, Karima Schwab Tags: Neurobiology Source Type: research

Ligand bias in receptor tyrosine kinase signaling [Signal Transduction]
Ligand bias is the ability of ligands to differentially activate certain receptor signaling responses compared with others. It reflects differences in the responses of a receptor to specific ligands and has implications for the development of highly specific therapeutics. Whereas ligand bias has been studied primarily for G protein–coupled receptors (GPCRs), there are also reports of ligand bias for receptor tyrosine kinases (RTKs). However, the understanding of RTK ligand bias is lagging behind the knowledge of GPCR ligand bias. In this review, we highlight how protocols that were developed to study GPCR signaling can b...
Source: Journal of Biological Chemistry - December 25, 2020 Category: Chemistry Authors: Kelly Karl, Michael D. Paul, Elena B. Pasquale, Kalina Hristova Tags: JBC Reviews Source Type: research

Phosphorylation of SMURF2 by ATM exerts a negative feedback control of DNA damage response [DNA and Chromosomes]
Timely repair of DNA double-strand breaks (DSBs) is essential to maintaining genomic integrity and preventing illnesses induced by genetic abnormalities. We previously demonstrated that the E3 ubiquitin ligase SMURF2 plays a critical tumor suppressing role via its interaction with RNF20 (ring finger protein 20) in shaping chromatin landscape and preserving genomic stability. However, the mechanism that mobilizes SMURF2 in response to DNA damage remains unclear. Using biochemical approaches and MS analysis, we show that upon the onset of the DNA-damage response, SMURF2 becomes phosphorylated at Ser384 by ataxia telangiectas...
Source: Journal of Biological Chemistry - December 25, 2020 Category: Chemistry Authors: Liu-Ya Tang, Adam Thomas, Ming Zhou, Ying E. Zhang Tags: Signal Transduction Source Type: research

Seeded fibrils of the germline variant of human {lambda}-III immunoglobulin light chain FOR005 have a similar core as patient fibrils with reduced stability [Molecular Biophysics]
Systemic antibody light chains (AL) amyloidosis is characterized by deposition of amyloid fibrils derived from a particular antibody light chain. Cardiac involvement is a major risk factor for mortality. Using MAS solid-state NMR, we studied the fibril structure of a recombinant light chain fragment corresponding to the fibril protein from patient FOR005, together with fibrils formed by protein sequence variants that are derived from the closest germline (GL) sequence. Both analyzed fibril structures were seeded with ex-vivo amyloid fibrils purified from the explanted heart of this patient. We find that residues 11-42 and ...
Source: Journal of Biological Chemistry - December 25, 2020 Category: Chemistry Authors: Teȷaswini Pradhan, Karthikeyan Annamalai, Riddhiman Sarkar, Stefanie Huhn, Ute Hegenbart, Stefan Schonland, Marcus Fandrich, Bernd Reif Tags: Protein Structure and Folding Source Type: research