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FEBS Letters

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https://www.readbyqxmd.com/read/28547778/deletion-of-hnf1%C3%AE-in-hepatocytes-results-in-fatty-liver-related-hepatocellular-carcinoma-in-mice
#1
LETTER
Qi Ni, Kai Ding, Ke-Qi Wang, Jin He, Chuan Yin, Jian Shi, Xin Zhang, Wei-Fen Xie, Yong-Quan Shi
Hepatocyte nuclear factor 1α (HNF1α) is a liver-enriched transcription factor that is critical for the maintenance of hepatocyte function. Our previous studies have demonstrated the therapeutic effects of HNF1α on hepatic fibrosis and hepatocellular carcinoma (HCC) in animals. In this study, we created hepatocyte-specific Hnf1α knockout mice using the Cre-loxP recombination system. The knockout mice display increased fatty acid synthesis in the liver. Moreover, these mice spontaneously develop HCC through fatty liver without cirrhosis...
May 26, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28543306/a-novel-c-src-recruitment-pathway-from-the-cytosol-to-focal-adhesions
#2
LETTER
Hiroaki Machiyama, Tomoyuki Yamaguchi, Tomonobu M Watanabe, Hideaki Fujita
The role of myristoylation in the localization and catalytic activity of Src at focal adhesions was investigated by live-cell imaging and site-directed mutagenesis. Although the majority of activated Src molecules are localized at focal adhesions, it is unclear how activated Src molecules are recruited to focal adhesions. Since Src is activated at the cell membrane, translocation of Src to cell membranes is thought to be essential for its recruitment to focal adhesions. Membrane-targeting-deficient Src mutant SrcG2A localizes at focal adhesions, indicating direct recruitment of Src from cytosol to focal adhesions...
May 25, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28542905/perfecting-prediction-of-mutational-impact-on-the-aggregation-propensity-of-the-als-associated-hnrnpa2-prion-like-protein
#3
Cristina Batlle, María Rosario Fernández, Valentin Iglesias, Salvador Ventura
An increasing number of human proteins are being found to bear a prion-like domain (PrLD) driving the formation of membraneless compartments through liquid-liquid phase separation. Point mutations in these PrLDs promote the transition to an amyloid-like state. There has been much debate on whether this aberrant aggregation is caused by compositional or sequential changes. A recent extensive mutational study of the ALS-associated prion-like hnRNPA2 protein provides a framework to discriminate the molecular determinants behind pathogenic PrLDs aggregation...
May 25, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28542723/spectroscopic-evidence-for-the-presence-of-a-high-valent-fe-iv-species-in-the-ferroxidase-reaction-of-an-archaeal-ferritin
#4
Kourosh Honarmand Ebrahimi, Eckhard Bill, Peter-Leon Hagedoorn, Wilfred R Hagen
A high-valent Fe(IV) species is proposed to be generated from the decay of a peroxodiferric intermediate in the catalytic cycle at the di-iron cofactor center of dioxygen activating enzymes such as methane monooxygenase. However, it is believed that this intermediate is not formed in the di-iron substrate site of ferritin, where oxidation of Fe(II) substrate to Fe(III) (ferroxidase reaction) occurs also via a peroxodiferric intermediate. In opposition to this generally accepted view, here we present evidence for the occurrence of a high-valent Fe(IV) in the ferroxidase reaction of an archaeal ferritin, which is based on trapped intermediates obtained with the freeze-quench technique and combination of spectroscopic characterization...
May 25, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28542702/chey-acetylation-is-required-for-ordinary-adaptation-time-in-e-coli-chemotaxis
#5
LETTER
Szilvia Baron, Michael Eisenbach
Recent studies demonstrated the dependence of speed adaptation in Escherichia coli on acetylation of the chemotaxis signaling molecule CheY. Here, we examined whether CheY acetylation is involved in chemotactic adaptation. A mutant lacking the acetylating enzyme acetyl-CoA synthetase (Acs) requires more time to adapt to attractant stimulation, and vice versa to repellent stimulation. This effect is avoided by conditions that favor production of acetyl-CoA, thus enabling Acs-independent CheY autoacetylation, or reversed by expressing Acs from a plasmid...
May 25, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28542725/nmr-studies-of-the-interaction-between-inner-membrane-associated-and-periplasmic-cytochromes-from-geobacter-sulfurreducens
#6
LETTER
Joana M Dantas, Anton Brausemann, Oliver Einsle, Carlos A Salgueiro
Geobacter sulfurreducens is a dissimilatory metal reducing bacterium with notable properties and significance in biotechnological applications. Biochemical studies suggest that the inner membrane-associated diheme cytochrome MacA and the periplasmic triheme cytochrome PpcA from G. sulfurreducens can exchange electrons. In this work, NMR chemical shift perturbation measurements were used to map the interface region and to measure the binding affinity between PpcA and MacA. The results show that MacA binds to PpcA in a cleft defined by hemes I and IV, favoring the contact between PpcA heme IV and the MacA high potential heme...
May 24, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28542817/c4b-binding-protein-negatively-regulates-the-tlr4-md-2-response-but-not-the-tlr3-response
#7
LETTER
Naoko Morita, Tatsuya Yamazaki, Yusuke Murakami, Ryutaro Fukui, Ikuko Yamai, Isao Ichimonji, Akina Nakashima, Fumiaki Nagaoka, Hidekazu Takagi, Kensuke Miyake, Sachiko Akashi-Takamura
Recently, we reported a novel function for C4b-binding protein (C4BP) in inhibiting the toll-like receptor (TLR)1/2 response by interacting with TLR2. TLRs share a common structure; hence, we examined the effect of C4BP on activation of other TLRs-TLR4 and TLR3. The results of immunoprecipitation assays suggest that C4BP interacts with TLR4/MD-2 but not TLR3. C4BP inhibits TLR4/MD-2-mediated, but not TLR3-mediated, pro-inflammatory cytokine production and nuclear factor (NF)-κB signaling. C4BP-deficient mice show increased interleukin (IL)-6 production in response to the TLR4/MD-2 ligand...
May 23, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28542779/downregulation-of-mir-199a-b-5p-is-associated-with-gcnt2-induction-upon-epithelial-mesenchymal-transition-in-colon-cancer
#8
LETTER
Chia-Chun Chao, Po-Han Wu, Hsiang-Chi Huang, Hsiao-Yu Chung, Yu-Chi Chou, Bi-He Cai, Reiji Kannagi
GCNT2, which encodes a key glycosyltransferase for blood group I antigen synthesis, is induced upon epithelial-mesenchymal transition (EMT). Our results indicate that GCNT2 is upregulated upon EMT induced with EGF and basic FGF in cultured human colon cancer cells. GCNT2 knockdown or overexpression decreases or increases, respectively, malignancy-related characteristics of colon cancer cells and I antigen levels. MiR-199a/b-5p is markedly downregulated upon EMT in colon cancer cells. Here, we find that miR-199a/b-5p consistently regulates GCNT2 expression in reporter assays and that it binds directly to the GCNT2 3'UTR intracellularly in RISC-trap assays...
May 23, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28542772/subcellular-localization-of-vip1-is-regulated-by-phosphorylation-and-14-3-3-proteins
#9
LETTER
Koichi Takeo, Takeshi Ito
Arabidopsis bZIP transcription factor VIRE2-INTERACTING PROTEIN 1 (VIP1) changes its localization from cytosol to nucleus when cells are subjected to mechanical or hypo-osmotic stress, though the mechanism of this change is not known. In this study, we show that change of VIP1 subcellular localization is synchronized with a change in the VIP1 phosphorylation state that is induced by mechanical/hypo-osmotic stress. VIP1 has three phosphorylatable serine residues in HXRXXS motifs, which are 14-3-3 binding targets...
May 23, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28543075/the-arabidopsis-guard-cell-outward-potassium-channel-gork-is-regulated-by-cpk33
#10
LETTER
Claire Corratgé-Faillie, Elsa Ronzier, Frédéric Sanchez, Karine Prado, Jeong-Hyeon Kim, Sophie Lanciano, Nathalie Leonhardt, Benoît Lacombe, Tou Cheu Xiong
A complex signaling network involving voltage-gated potassium channels from the Shaker family contributes to the regulation of stomatal aperture. Several kinases and phosphatases have been shown to be crucial for ABA-dependent regulation of the ion transporters. To date, the Ca(2+) -dependent regulation of Shaker channels by Ca(2+) -dependent protein kinases (CPKs) is still elusive. A functional screen in Xenopus oocytes was launched to identify such CPKs able to regulate the three main guard cell Shaker channels KAT1, KAT2 and GORK...
May 21, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28542876/hypothalamic-lipid-laden-astrocytes-induce-microglia-migration-and-activation
#11
LETTER
Yoon-Hee Kwon, Jiye Kim, Chu-Sook Kim, Thai Hien Tu, Min-Seon Kim, Kyungho Suk, Dong Hee Kim, Byung-Ju Lee, Hye-Seon Choi, Taesun Park, Myung-Sook Choi, Tsuyoshi Goto, Teruo Kawada, Tae-Youl Ha, Rina Yu
Obesity-induced hypothalamic inflammation is closely associated with various metabolic complications and neurodegenerative disorders. Astrocytes, the most abundant glial cells in the central nervous system, play a crucial role in pathological hypothalamic inflammatory processes. Here, we demonstrate that hypothalamic astrocytes accumulate lipid droplets under saturated fatty acid-rich conditions, such as obese environment, and that the lipid-laden astrocytes increase astrogliosis markers and inflammatory cytokines (TNFα, IL-1β, IL-6, MCP-1) at the transcript and/or protein level...
May 21, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28542875/structure-of-the-px-domain-of-snx25-reveals-a-novel-phospholipid-recognition-model-by-dimerization-in-the-px-domain
#12
LETTER
Kai Su, Tingting Xu, Zhijun Yu, Jiabin Zhu, Yulong Zhang, Minhao Wu, Ying Xiong, Jinsong Liu, Jinxin Xu
SNX25, an RGS-PX domain containing Sorting Nexin (SNX) member, has been proposed to be involved in the lysosomal degradation of the TGF-β receptor and the development of temporal lobe epilepsy. Targeting to the endosomal membranes by the specific binding of phosphorylated phosphatidylinositols (PIs) through the PX domain is critical for the function of SNXs. However, the mechanism for SNX25-PX targeting to the endosomes remains unclear. Here, we demonstrate that the PX domain of zebrafish SNX25 (zSNX25-PX) is capable of binding to PI3P only in its dimeric form...
May 21, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28542810/dnmt1-cooperates-with-mbd4-to-inhibit-the-expression-of-glucocorticoid-induced-tnfr-related-protein-in-human-t-cells
#13
LETTER
Shuaiwei Wang, Yangyang Li, Fangming Zhu, Fang Lin, Xuerui Luo, Binbin Zhao, Peng Zhang, Dan Li, Yayi Gao, Rui Liang, Luyan Liu, Andy Tsun, Xiaojun Yuan, Kejin Wu, Bin Li
Glucocorticoid-induced TNFR-related protein (GITR) is constitutively expressed in T regulatory (Treg) cells and regulates their suppressive function. We identified two methylated CpG islands in the Gitr locus. Using a ChIP assay, we demonstrate that both DNMT1 and MBD4 bind to the Gitr promoter. Moreover, knockdown of DNMT1 decreases the binding activity of MBD4. We observed much higher levels of both DNMT1 and MBD4 in human CD4(+) CD25(-) conventional T (Tconv) cells. Moreover, co-overexpression of DNMT1 and MBD4 in Treg cells significantly inhibits GITR expression and impairs their suppressive activity...
May 21, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28524232/robust-ir-based-detection-of-stable-and-fractionally-populated-g-c-and-a-t-hoogsteen-base-pairs-in-duplex-dna
#14
LETTER
Allison L Stelling, Yu Xu, Huiqing Zhou, Seung H Choi, Mary C Clay, Dawn K Merriman, Hashim M Al-Hashimi
Non-canonical G-C(+) and A-T Hoogsteen base pairs can form in duplex DNA and play roles in recognition, damage repair, and replication. Identifying Hoogsteen base pairs in DNA duplexes remains challenging due to difficulties in resolving syn versus anti purine bases with X-ray crystallography; and size limitations and line broadening can make them difficult to characterize by NMR spectroscopy. Here, we show how infrared (IR) spectroscopy can identify G-C(+) and A-T Hoogsteen base pairs in duplex DNA across a range of different structural contexts...
May 19, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28524231/comparison-of-pre-ribosomal-rna-processing-pathways-in-yeast-plant-and-human-cells-focus-on-coordinated-action-of-endo-and-exoribonucleases
#15
REVIEW
Rafal Tomecki, Pawel J Sikorski, Monika Zakrzewska-Placzek
Proper regulation of ribosome biosynthesis is mandatory for cellular adaptation, growth and proliferation. Ribosome biogenesis is the most energetically demanding cellular process, which requires tight control. Abnormalities in ribosome production have severe consequences, including developmental defects in plants and genetic diseases (ribosomopathies) in humans. One of the processes occurring during eukaryotic ribosome biogenesis is processing of the ribosomal RNA precursor molecule (pre-rRNA), synthesized by RNA polymerase I, into mature rRNAs...
May 19, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28524228/structure-and-characterization-of-a-nad-p-h-dependent-carbonyl-reductase-from-pseudomonas-aeruginosa-pao1
#16
LETTER
Shanshan Li, Xiaozhen Teng, Li Su, Guannan Mao, Yueyang Xu, Tingting Li, Riuhua Liu, Qionglin Zhang, Yingying Wang, Mark Bartlam
To investigate the function of the pa4079 gene from the opportunistic pathogen Pseudomonas aeruginosa PAO1, we determined its crystal structure and confirmed it to be a NAD(P)-dependent short-chain dehydrogenase/reductase. Structural similarity and activity for a broad range of substrates indicate that PA4079 functions as a carbonyl reductase. Comparison of apo- and holo-PA4079 shows that NADP stabilises the active site specificity loop, and small molecule binding induces rotation of the Tyr183 side chain by approximately 90(°) out of the active site...
May 19, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28524227/computational-approaches-for-interpreting-scrna-seq-data
#17
REVIEW
R Rostom, V Svensson, S A Teichmann, G Kar
The recent developments in high throughput single-cell RNA sequencing technology (scRNA-seq) have enabled the generation of vast amounts of transcriptomic data at cellular resolution. With these advances come new modes of data analysis, building on high-dimensional data mining techniques. Here, we consider biological questions for which scRNA-seq data is used, both at a cell and gene level, and describe tools available for these types of analyses. This is an exciting and rapidly evolving field, where clustering, pseudotime inference, branching inference and gene-level analyses are particularly informative areas of computational analysis...
May 19, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28504339/mexneurin-is-a-novel-precursor-of-peptides-in-the-central-nervous-system-of-rodents
#18
LETTER
Maura Epifanía Matus-Ortega, Philippe Leff Gelman, Juan Carlos Calva-Nieves, Anabel Flores-Zamora, Alberto Salazar-Juárez, Carlos-Alejandro Torner-Aguilar, Gerardo Gamba, Paola De Los Heros, Bonnie Peng, John E Pintar, Heinrich S Gompf, Charles N Allen, Benito Antón-Palma
Endomorphins have been proposed as the endogenous ligand agonists of the μ-opioid receptor; however, no propeptide precursor protein for endomorphins has been identified. Here, to identify the presumed precursor of endomorphins, we designed an immunoscreening assay using specific affinity-purified rabbit antisera raised against synthetic endomorphins in a whole mouse brain cDNA library. Following this approach, we identifiy a DNA sequence encoding a protein precursor, which we name proMexneurin, that contains three different peptide sequences: Mexneurin-1 (an endomorphin-like peptide), Mexneurin-2, and Mexneurin-3, a peptide which appears to be unrelated to endomorphins...
May 15, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28504316/rational-design-of-a-ph-insensitive-cyan-fluorescent-protein-cypet2-based-on-the-cypet-crystal-structure
#19
LETTER
Rui Liu, Xiao-Jian Hu, Yu Ding
The emission spectrum of widely used CyPet is pH-sensitive. In order to synthesize a pH-insensitive cyan fluorescent protein by rational design, we solved the crystal structures of CyPet under different pH conditions. The indole group of the CyPet chromophore adopts a cis-coplanar conformation in acidic and neutral conditions, while it converts to trans-coplanar under basic conditions. His148 and Glu222 play a vital role in this isomerization. The pH-sensitive chromophore isomerization and change in the emission spectrum can be explained by the co-existence of several different fluorescent states...
May 15, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28504309/deletion-of-the-short-n-terminal-extension-in-ocp-reveals-the-main-site-for-frp-binding
#20
LETTER
Nikolai N Sluchanko, Yury B Slonimskiy, Marcus Moldenhauer, Thomas Friedrich, Eugene G Maksimov
The Orange Carotenoid Protein (OCP) plays a key role in cyanobacterial photoprotection. Photoconversion entails structural rearrangements in OCP that are required for its binding to phycobilisome, thereby inducing excitation energy dissipation. Detachment of OCP from phycobilisome requires the fluorescence recovery protein (FRP). It is considered that OCP interacts with FRP only in the photoactivated state; however, the binding site for FRP is currently unknown. As an important stabilizing element in orange OCP, the short αA-helix within the N-terminal extension (NTE) binds to the C-terminal domain (CTD, but unfolds upon photoactivation and interferes with phycobilisome binding...
May 15, 2017: FEBS Letters
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