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Development of a specific live-cell assay for native autophagic flux.

Nathaniel Safren, Elizabeth M Tank, Ahmed M Malik, Jason P Chua, Nicholas Santoro, Sami J Barmada,

Autophagy is an evolutionarily conserved pathway mediating the breakdown of cellular proteins and organelles. Emphasizing its pivotal nature, autophagy dysfunction contributes to many diseases; nevertheless, development of effective autophagy modulating drugs is hampered by fundamental deficiencies in available methods for measuring autophagic activity, or flux. To overcome these limitations, we ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :101003]

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Solution structures of human myeloma IgG3 antibody reveal extended Fab and Fc regions relative to the other IgG subclasses.

Valentina A Spiteri, Margaret Goodall, James Doutch, Robert P Rambo, Jayesh Gor, Stephen J Perkins,

Human immunoglobulin IgG3 possesses a uniquely long hinge region that separates its Fab antigen-binding and Fc receptor-binding regions. Owing to this hinge length, the molecular structure of full-length IgG3 remains elusive, and the role of the two conserved glycosylation sites in the Fc region is unknown. To address these issues, ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100995]

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A Cas12a-based CRISPR interference system for multigene regulation in mycobacteria.

Neil Fleck, Christoph Grundner,

Mycobacteria are responsible for a heavy global disease burden, but their relative genetic intractability has long frustrated many research efforts. The introduction of CRISPR interference (CRISPRi) has made gene repression in mycobacteria much more efficient, but limitations of the prototypical Cas9-based platform, for example in multigene regulation, remain. Here, we ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100990]

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Structural and functional analysis of gum arabic l-rhamnose-α-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family.

Tatsuya Kondo, Miyu Kichijo, Akiho Maruta, Makoto Nakaya, Shigeo Takenaka, Takatoshi Arakawa, Shinya Fushinobu, Tatsuji Sakamoto,

Gum arabic (GA) is widely used as an emulsion stabilizer and coating in several industrial applications, such as foods and pharmaceuticals. GA contains a complex carbohydrate moiety, and the non-reducing ends of the side chains are often capped with l-rhamnose; thus, enzymes that can remove these caps are promising tools ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :101001]

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Neurological impairment caused by Schistosoma mansoni systemic infection exhibits early features of idiopathic neurodegenerative disease.

Juciano Gasparotto, Mario Roberto Senger, Emilio Telles de Sá Moreira, Pedro Ozorio Brum, Flávio Gabriel Carazza Kessler, Daniel Oppermann Peixoto, Alana Castro Panzenhagen, Lin Kooi Ong, Marlene Campos Soares, Patricia Alves Reis, Giuliana Viegas Schirato, Walter César Góes Valente, Bogar Omar Araújo Montoya, Floriano P Silva, José Claudio Fonseca Moreira, Felipe Dal-Pizzol, Hugo C Castro-Faria-Neto, Daniel Pens Gelain,

Schistosomiasis, a neglected tropical disease caused by trematodes of the Schistosoma genus, affects over 250 million people around the world. This disease has been associated with learning and memory deficits in children, while reduced attention levels, impaired work capacity, and cognitive deficits have been observed in adults. Strongly correlated with ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100979]

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The lncRNA HMS recruits RNA binding protein HuR to stabilize the 3'-UTR of HOXC10 mRNA.

Priyanka Priyanka, Madhur Sharma, Sanjeev Das, Sandeep Saxena,

Long non-coding RNAs (lncRNAs) have been reported to drive key cancer pathways but the functions of majority of lncRNAs are unknown making a case for comprehensive functional evaluation of lncRNAs. With an aim to identify lncRNAs dysregulated in human cancers we analyzed the cancer patient database of lung adenocarcinoma (LUAD) ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100997]

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Delivering progranulin to neuronal lysosomes protects against excitotoxicity.

Skylar E Davis, Jonathan R Roth, Qays Aljabi, Ahmad R Hakim, Katherine E Savell, Jeremy J Day, Andrew E Arrant,

Loss-of-function mutations in progranulin (GRN) are a major genetic cause of frontotemporal dementia (FTD), possibly due to loss of progranulin's neurotrophic and anti-inflammatory effects. Progranulin promotes neuronal growth and protects against excitotoxicity and other forms of injury. It is unclear if these neurotrophic effects are mediated through cellular signaling or ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100993]

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Insulin-induced genes INSIG1 and INSIG2 mediate oxysterol-dependent activation of the PERK/eIF2α/ATF4 axis.

Yuichi Watanabe, Takashi Sasaki, Shoko Miyoshi, Makoto Shimizu, Yoshio Yamauchi, Ryuichiro Sato,

Insulin-induced genes (INSIGs) encode endoplasmic reticulum (ER)-resident proteins that regulate intracellular cholesterol metabolism. Oxysterols are oxygenated derivatives of cholesterol, some of which orchestrate lipid metabolism via interaction with INSIGs. Recently, it was reported that expression of activating transcription factor-4 (ATF4) was induced by certain oxysterols; the precise of mechanism is ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100989]

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Letting go: Deep Computational Modeling Insights into pH-Dependent Calcium Affinity.

Matthias Buck,

Calcium and other cofactors can feature as key additions to a molecular interface, to the extent that the cofactor is completely buried in the bound state. How can such an interaction be regulated then? The answer: By facilitating a switch through an allosteric network. While a number of unbinding mechanisms ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100974]

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Basic residues at the C-gate of DNA gyrase are involved in DNA supercoiling.

Eric M Smith, Alfonso Mondragón,

DNA gyrase is a type II topoisomerase that is responsible for maintaining the topological state of bacterial and some archaeal genomes. It uses an ATP-dependent two-gate strand passage mechanism that is shared among all type II topoisomerases. During this process DNA gyrase creates a transient break in the DNA, the ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :101000]

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An 'up' oriented methionine-aromatic structural motif in SUMO is critical for its stability and activity.

Kiran Sankar Chatterjee, Ranabir Das,

Protein structural bioinformatic analyses suggest preferential associations between methionine and aromatic amino acid residues in proteins. Ab initio energy calculations highlight a conformation-dependent stabilizing interaction between the interacting sulfur-aromatic molecular pair. However, the relevance of buried methionine-aromatic motifs to protein folding and function is relatively unexplored. The Small Ubiquitin-Like Modifier ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100970]

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Interdomain Flexibility and Interfacial Integrity of β-Lactamase Inhibitory Protein (BLIP) Modulate Its Binding to Class A β-Lactamases.

Liwen Huang, Pui-Kin So, Yu Wai Chen, Yun-Chung Leung, Zhong-Ping Yao,

β-Lactamase inhibitory protein (BLIP) consists of a tandem repeat of αβ domains conjugated by an interdomain loop and can effectively bind and inactivate class A β-lactamases, which are responsible for resistance of bacteria to β-lactam antibiotics. The varied ability of BLIP to bind different β-lactamases and the structural determinants for ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100980]

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PTEN regulates adipose progenitor cell growth, differentiation, and replicative aging.

Anna S Kirstein, Stephanie Kehr, Michèle Nebe, Martha Hanschkow, Lisa A G Barth, Judith Lorenz, Melanie Penke, Jana Breitfeld, Diana Le Duc, Kathrin Landgraf, Antje Körner, Peter Kovacs, Peter F Stadler, Wieland Kiess, Antje Garten,

The tumor suppressor phosphatase and tensin homolog (PTEN) negatively regulates the insulin signaling pathway. Germline PTEN pathogenic variants cause PTEN Hamartoma Tumor Syndrome (PHTS), associated with lipoma development in children. Adipose progenitor cells (APCs) lose their capacity to differentiate into adipocytes during continuous culture, while APCs from PHTS patients' lipomas ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100968]

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High salt transcription of DNA co-tethered with T7 RNA polymerase to beads generates increased yields of highly pure RNA.

Elvan Cavac, Luis E Ramírez-Tapia, Craig T Martin,

High yields of RNA are routinely prepared following the two-step approach of high-yield in vitro transcription using T7 RNA polymerase followed by extensive purification using gel separation or chromatographic methods. We recently demonstrated that in high-yield transcription reactions, as RNA accumulates in solution, T7 RNA polymerase rebinds and extends the ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100999]

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CDC5L promotes early chondrocyte differentiation and proliferation by modulating pre-mRNA splicing of SOX9, COL2A1, and WEE1.

Go Jokoji, Shingo Maeda, Kazuki Oishi, Toshiro Ijuin, Masahiro Nakajima, Hiroki Tawaratsumida, Ichiro Kawamura, Hiroyuki Tominaga, Eiji Taketomi, Shiro Ikegawa, Noboru Taniguchi,

Ossification of the posterior longitudinal ligament (OPLL) of the spine is a common pathological condition that causes intractable myelopathy and radiculopathy, mainly the result of an endochondral ossification-like process. Our previous genome-wide association study identified six susceptibility loci for OPLL, including the CDC5L gene region. Here, we found CDC5L to ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100994]

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The BTB-domain transcription factor ZBTB2 recruits chromatin remodelers and a histone chaperone during the exit from pluripotency.

Daniel Olivieri, Sujani Paramanathan, Anaïs F Bardet, Daniel Hess, Sébastien A Smallwood, Ulrich Elling, Joerg Betschinger,

Transcription factors (TFs) harboring BTB (Broad-Complex, Tramtrack, and Bric a brac) domains play important roles in development and disease. These BTB domains are thought to recruit transcriptional modulators to target DNA regions. However, a systematic molecular understanding of the mechanism of action of this TF family is lacking. Here, we ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100947]

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Interactions between semaphorins and plexin/neuropilin receptor complexes in the membranes of live cells.

Shaun M Christie, Jing Hao, Erin Tracy, Matthias Buck, Jennifer S Yu, Adam W Smith,

Signaling of semaphorin ligands via their plexin/neuropilin receptors is involved in tissue patterning in the developing embryo. These proteins play roles in cell migration and adhesion, but are also important in disease etiology, including in cancer angiogenesis and metastasis. While some structures of the soluble domains of these receptors have ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100965]

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HSP90 inhibition downregulates DNA replication and repair genes via E2F1 repression.

Hanqing Liu, Ziwen Lu, Xiaofeng Shi, Lanlan Liu, Peishan Zhang, Erica A Golemis, Zhigang Tu,

Mantle cell lymphoma (MCL) is an especially aggressive and highly heterogeneous mature B cell lymphoma. Heat shock protein 90 (HSP90) is considered an attractive therapeutic target in a variety of cancers, including MCL, but no HSP90 inhibitors have succeeded in the clinical trials to date. Exploring fine mechanisms of HSP90 ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100996]

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Heparan sulfate promotes differentiation of white adipocytes to maintain insulin sensitivity and glucose homeostasis.

Takuro Matsuzawa, Masanobu Morita, Ai Shimane, Rina Otsuka, Yu Mei, Fumitoshi Irie, Yu Yamaguchi, Kazuhiko Yanai, Takeo Yoshikawa,

Heparan sulfate (HS), a highly sulfated linear polysaccharide, is involved in diverse biological functions in various tissues. Although previous studies have suggested a possible contribution of HS to the differentiation of white adipocytes, there has been no direct evidence supporting this. Here, we inhibited the synthesis of HS chains in ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :101006]

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Structural basis for template switching by a group II intron-encoded non-LTR-retroelement reverse transcriptase.

Alfred M Lentzsch, Jennifer L Stamos, Jun Yao, Rick Russell, Alan M Lambowitz,

Reverse transcriptases (RTs) can switch template strands during cDNA synthesis, enabling them to join discontinuous nucleic acid sequences. Template switching plays crucial roles in retroviral replication and recombination, is used for adapter addition in RNA-seq, and may contribute to retroelement fitness by increasing evolutionary diversity and enabling continuous cDNA synthesis ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100971]

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OdoriFy: A conglomerate of Artificial Intelligence-driven prediction engines for olfactory decoding.

Ria Gupta, Aayushi Mittal, Vishesh Agrawal, Sushant Gupta, Krishan Gupta, Rishi Raj Jain, Prakriti Garg, Sanjay Kumar Mohanty, Riya Sogani, Harshit Singh Chhabra, Vishakha Gautam, Tripti Mishra, Debarka Sengupta, Gaurav Ahuja,

The molecular mechanisms of olfaction, or the sense of smell, are relatively under-explored compared to other sensory systems, primarily due to its underlying molecular complexity and the limited availability of dedicated predictive computational tools. Odorant receptors allow the detection and discrimination of a myriad of odorant molecules and therefore mediate ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100956]

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Role of sequence and position of the cleavage sites in prothrombin activation.

Bosko M Stojanovski, Enrico Di Cera,

In the penultimate step of the coagulation cascade, the multidomain vitamin-K dependent zymogen prothrombin is converted to thrombin by the prothrombinase complex composed of factor Xa, cofactor Va and phospholipids. Activation of prothrombin requires cleavage at two residues, R271 and R320, along two possible pathways generating either the intermediate prethrombin-2 ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100955]

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The active component of Ginseng, Ginsenoside Rb1, improves erythropoiesis in models of Diamond Blackfan Anemia by targeting Nemo-like Kinase.

Mark C Wilkes, Kevin Jung, Britney E Lee, Mallika Saxena, Ryan S Sathianathen, Jacqueline D Mercado, Cristina Perez, Johan Flygare, Anupama Narla, Bertil Glader, Kathleen M Sakamoto,

Nemo-like kinase (NLK) is a member of the MAPK family of kinases and shares a highly conserved kinase domain with other MAPK family members. The activation of NLK contributes to the pathogenesis of Diamond Blackfan Anemia (DBA), reducing c-myb expression and mTOR activity, and is therefore a potential therapeutic target. ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100988]

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Oscillation of Cdc20-APC/C-mediated CAMDI stability is critical for cortical neuron migration.

Shohei Okuda, Mariko Sato, Saho Kato, Shun Nagashima, Ryoko Inatome, Shigeru Yanagi, Toshifumi Fukuda,

Radial migration during cortical development is required for formation of the six-layered structure of the mammalian cortex. Defective migration of neurons is linked to several developmental disorders such as autism and schizophrenia. A unique swollen structure called the dilation is formed in migrating neurons and is required for movement of ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :100986]

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Metformin inhibits MAPK signaling and rescues pancreatic Aquaporin 7 expression to induce insulin secretion in type 2 diabetes mellitus.

Xueting He, Fei Gao, Jiaojiao Hou, Tingjie Li, Jiang Tan, Chunyu Wang, Xiaoyan Liu, Maoqi Wang, Hui Liu, Yuqin Chen, Zhuoyuan Yu, Mei Yang,

Metformin is the first-line anti-diabetic agent for type 2 diabetes mellitus (T2DM) treatment. Although accumulated evidence has shed light on the consequences of metformin action, the precise mechanisms of its action, especially in the pancreas, are not fully understood. Aquaporin 7 (AQP7) acts as a critical regulator of intra-islet glycerol ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2021, :101002]

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