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https://www.readbyqxmd.com/read/27920251/a-homeostatic-shift-facilitates-endoplasmic-reticulum-proteostasis-through-transcriptional-integration-of-proteostatic-stress-response-pathways
#1
Liam Baird, Tadayuki Tsujita, Eri Kobayashi, Ryo Funayama, Takeshi Nagashima, Keiko Nakayama, Masayuki Yamamoto
Eukaryotic cells maintain protein homeostasis through the activity of multiple basal and inducible systems, which function in concert to allow cells to adapt to a wide range of environmental conditions. Whilst the transcriptional programs regulating individual pathways have been studied in detail, it is not known how the different pathways are transcriptionally integrated such that a deficiency in one pathway can be compensated by a change in an auxiliary response. One such pathway that plays an essential role in many proteostasis responses is the ubiquitin-proteasome system (UPS), which functions to degrade damaged, unfolded or short half-life proteins...
December 5, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27920157/two-serk-receptor-like-kinases-interact-with-the-receptor-like-kinase-ems1-in-anther-cell-fate-determination
#2
Zhiyong Li, Yao Wang, Jian Huang, Nagib Ahsan, Gabriel Biener, Joel Paprocki, Jay J Thelen, Valerica Raicu, Dazhong Zhao
Cell signaling pathways mediated by leucine-rich repeat receptor-like kinases (LRR-RLK) are essential for plant growth, development and defense. The EMS1 (EXCESS MICROSPOROCYTES1) LRR-RLK and its small protein ligand TPD1 (TAPETUM DETERMINANT1) play a fundamental role in somatic and reproductive cell differentiation during early anther development in Arabidopsis (Arabidopsis thaliana). However, it is unclear whether other cell surface molecules serve as co-regulators of EMS1. Here, we show that SERK1 (SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE1) and SERK2 LRR-RLKs act redundantly as co-regulatory and physical partners of EMS1...
December 5, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27917194/a-network-approach-of-gene-co-expression-in-the-zea-mays-aspergillus-flavus-pathosystem-to-map-host-pathogen-interaction-pathways
#3
Bryan M Musungu, Deepak Bhatnagar, Robert L Brown, Gary A Payne, Greg OBrian, Ahmad M Fakhoury, Matt Geisler
A gene co-expression network (GEN) was generated using a dual RNA-seq study with the fungal pathogen Aspergillus flavus and its plant host Zea mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network revealed a high degree of connectivity in many of the previously recognized pathways in Z. mays such as jasmonic acid, ethylene, and reactive oxygen species (ROS). For the pathogen A. flavus, a link between aflatoxin production and vesicular transport was identified within the network...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27909043/an-atlas-of-human-kinase-regulation
#4
David Ochoa, Mindaugas Jonikas, Robert T Lawrence, Bachir El Debs, Joel Selkrig, Athanasios Typas, Judit Villén, Silvia Dm Santos, Pedro Beltrao
The coordinated regulation of protein kinases is a rapid mechanism that integrates diverse cues and swiftly determines appropriate cellular responses. However, our understanding of cellular decision-making has been limited by the small number of simultaneously monitored phospho-regulatory events. Here, we have estimated changes in activity in 215 human kinases in 399 conditions derived from a large compilation of phosphopeptide quantifications. This atlas identifies commonly regulated kinases as those that are central in the signaling network and defines the logic relationships between kinase pairs...
December 1, 2016: Molecular Systems Biology
https://www.readbyqxmd.com/read/27908826/itraq-based-quantitative-proteomic-analysis-of-midgut-in-silkworm-infected-with-bombyx-mori-cytoplasmic-polyhedrosis-virus
#5
Kun Gao, Xiang-Yuan Deng, Meng-Ke Shang, Guang-Xing Qin, Cheng-Xiang Hou, Xi-Jie Guo
: Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) specifically infects the epithelial cells in the midgut of silkworm and causes them to death, which negatively affects the sericulture industry. In order to determine the midgut response at the protein levels to the virus infection, differential proteomes of the silkworm midgut responsive to BmCPV infection were identified with isobaric tags for relative and absolute quantitation (iTRAQ) labeling followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS)...
November 28, 2016: Journal of Proteomics
https://www.readbyqxmd.com/read/27903230/glucocorticoid-receptor-interacting-co-regulators-putative-candidates-for-future-drug-targeting-therapy
#6
Alessia Di Silvestre, Marianna Lucafò, Sara De Iudicibus, Alessandro Ventura, Stefano Martelossi, Gabriele Stocco, Giuliana Decorti
Glucocorticoids (GCs) are largely used in different inflammatory, autoimmune and proliferative diseases. To date their mechanism of action is not completely clear and more studies are necessary, in particular to explain the great interindividual variability in clinical response. In this panorama the glucocorticoid receptor (GR) has an important role: in fact it regulates the pharmacological response thanks to the capability to interact with different molecules (DNA, RNA, ncRNA and proteins) that are known to influence its activity...
November 29, 2016: Mini Reviews in Medicinal Chemistry
https://www.readbyqxmd.com/read/27902780/co-regulation-of-iron-metabolism-and-virulence-associated-functions-by-iron-and-xibr-a-novel-iron-binding-transcription-factor-in-the-plant-pathogen-xanthomonas
#7
Sheo Shankar Pandey, Pradeep Kumar Patnana, Santosh Kumar Lomada, Archana Tomar, Subhadeep Chatterjee
Abilities of bacterial pathogens to adapt to the iron limitation present in hosts is critical to their virulence. Bacterial pathogens have evolved diverse strategies to coordinately regulate iron metabolism and virulence associated functions to maintain iron homeostasis in response to changing iron availability in the environment. In many bacteria the ferric uptake regulator (Fur) functions as transcription factor that utilize ferrous form of iron as cofactor to regulate transcription of iron metabolism and many cellular functions...
November 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27899633/jmjd6-and-u2af65-co-regulate-alternative-splicing-in-both-jmjd6-enzymatic-activity-dependent-and-independent-manner
#8
Jia Yi, Hai-Feng Shen, Jin-Song Qiu, Ming-Feng Huang, Wen-Juan Zhang, Jian-Cheng Ding, Xiao-Yan Zhu, Yu Zhou, Xiang-Dong Fu, Wen Liu
JMJD6, a jumonji C (Jmj C) domain-containing protein demethylase and hydroxylase, has been implicated in an array of biological processes. It has been shown that JMJD6 interacts with and hydroxylates multiple serine/arginine-rich (SR) proteins and SR related proteins, including U2AF65, all of which are known to function in alternative splicing regulation. However, whether JMJD6 is widely involved in alternative splicing and the molecular mechanism underlying JMJD6-regulated alternative splicing have remained incompletely understood...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898286/a-conserved-puccinia-striiformis-protein-interacts-with-wheat-npr1-and-reduces-induction-of-pathogenesis-related-genes-in-response-to-pathogens
#9
Xiaodong Wang, Baoju Yang, Kun Li, Zhensheng Kang, Dario Cantu, Jorge Dubcovsky
In Arabidopsis, NPR1 is a key transcriptional co-regulator of systemic acquired resistance. Upon pathogen challenge, NPR1 translocates from the cytoplasm to the nucleus, where it interacts with TGA-bZIP transcription factors to activate the expression of several Pathogenesis-Related (PR) genes. In a screen of a yeast two-hybrid library from wheat leaves infected with Puccinia striiformis f. sp. tritici, we identified a conserved rust protein that interacts with wheat NPR1 and named it Puccinia NPR1 interactor (PNPi)...
November 29, 2016: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/27891125/poly-%C3%AE-glutamic-acids-contribute-to-biofilm-formation-and-plant-root-colonization-in-selected-environmental-isolates-of-bacillus-subtilis
#10
Yiyang Yu, Fang Yan, Yun Chen, Christopher Jin, Jian-Hua Guo, Yunrong Chai
Bacillus subtilis is long known to produce poly-γ-glutamic acids (γ-PGA) as one of the major secreted polymeric substances. In B. subtilis, the regulation of γ-PGA production and its physiological role are still unclear. B. subtilis is also capable of forming structurally complex multicellular communities, or biofilms, in which an extracellular matrix consisting of secreted proteins and polysaccharides holds individual cells together. Biofilms were shown to facilitate B. subtilis-plant interactions. In this study, we show that different environmental isolates of B...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27886276/estradiol-estrogen-receptor-%C3%AE-mediates-the-expression-of-the-cxxc5-gene-through-the-estrogen-response-element-dependent-signaling-pathway
#11
Pelin Yaşar, Gamze Ayaz, Mesut Muyan
17β-estradiol (E2), the primary circulating estrogen hormone, mediates physiological and pathophysiological functions of breast tissue mainly through estrogen receptor α (ERα). Upon binding to E2, ERα modulates the expression of target genes involved in the regulation of cellular proliferation primarily through interactions with specific DNA sequences, estrogen response elements (EREs). Our previous microarray results suggested that E2-ERα modulates CXXC5 expression. Because of the presence of a zinc-finger CXXC domain (ZF-CXXC), CXXC5 is considered to be a member of the ZF-CXXC family, which binds to non-methylated CpG dinucleotides...
November 25, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27886269/in-silico-clustering-of-salmonella-global-gene-expression-data-reveals-novel-genes-co-regulated-with-the-spi-1-virulence-genes-through-hild
#12
Irma Martínez-Flores, Deyanira Pérez-Morales, Mishael Sánchez-Pérez, Claudia C Paredes, Julio Collado-Vides, Heladia Salgado, Víctor H Bustamante
A wide variety of Salmonella enterica serovars cause intestinal and systemic infections to humans and animals. Salmonella Patogenicity Island 1 (SPI-1) is a chromosomal region containing 39 genes that have crucial virulence roles. The AraC-like transcriptional regulator HilD, encoded in SPI-1, positively controls the expression of the SPI-1 genes, as well as of several other virulence genes located outside SPI-1. In this study, we applied a clustering method to the global gene expression data of S. enterica serovar Typhimurium from the COLOMBOS database; thus genes that show an expression pattern similar to that of SPI-1 genes were selected...
November 25, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27881075/modelling-microbial-metabolic-rewiring-during-growth-in-a-complex-medium
#13
Marco Fondi, Emanuele Bosi, Luana Presta, Diletta Natoli, Renato Fani
BACKGROUND: In their natural environment, bacteria face a wide range of environmental conditions that change over time and that impose continuous rearrangements at all the cellular levels (e.g. gene expression, metabolism). When facing a nutritionally rich environment, for example, microbes first use the preferred compound(s) and only later start metabolizing the other one(s). A systemic re-organization of the overall microbial metabolic network in response to a variation in the composition/concentration of the surrounding nutrients has been suggested, although the range and the entity of such modifications in organisms other than a few model microbes has been scarcely described up to now...
November 24, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27878298/trail-overexpression-co-regulated-by-egr1-and-hre-enhances-radiosensitivity-of-hypoxic-a549-cells-depending-on-its-apoptosis-inducing-role
#14
Yan-Ming Yang, Fang Fang, Xin Li, Lei Yu, Zhi-Cheng Wang
Ionizing radiation can upregulate the expression levels of TRAIL and enhance tumor cell apoptosis. While Early growth response 1 (Egr1) gene promoter has radiation inducible characteristics, the expression for exogenous gene controlled by Egr1 promoter could be enhanced by ionizing radiation, but its efficiency is limited by tissue hypoxia. Hypoxia response elements (HREs) are important hypoxic response regulatory sequences and sensitivity enhancers. Therefore, we chose TRAIL as the gene radiotherapy to observe whether it is regulated by Egr1 and HER and its effects on A549 cells and its mechanism...
November 23, 2016: Oncology Reports
https://www.readbyqxmd.com/read/27872245/the-transcription-factor-athb5-affects-ga-mediated-plasticity-in-hypocotyl-cell-growth-during-seed-germination
#15
Petra Stamm, Alexander T Topham, Nur K Mukhtar, Matthew Jackson, Daniel Tome, Jim L Beynon, George W Bassel
The seed to seedling transition is driven exclusively by cell shape changes within the axis of the plant embryo. Using digital single cell analysis of 3D cellular growth, here we identify the presence of two spatially and temporally distinct cell expansion modules within subdomains of the growing embryo. The second growth module is within the hypocotyl and drives the final phase of the completion of germination under optimal conditions. Using network inference, we identified the transcription factor ATHB5 as a genetic factor specifically induced and localized to the hypocotyl prior to its expansion...
November 21, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27864379/foxn4-promotes-gene-expression-required-for-multiple-motile-cilia-formation
#16
Evan P Campell, Ian K Quigley, Chris Kintner
Multiciliated cell (MCC) differentiation involves extensive organelle biogenesis required to extend hundreds of motile cilia. Key transcriptional regulators have been identified that drive gene expression required for organelle biogenesis during MCC differentiation, which are activated by, and act downstream, of two related, small coiled-coil proteins, Multicilin and Gemc1. Here we identify foxn4 as a new downstream target of Multicilin required for MCC differentiation in the Xenopus skin. When Foxn4 activity is inhibited in Xenopus embryos, MCCs show transient ciliogenesis defects similar to those observed in mutants in Foxj1, a known key regulator of genes required for motile ciliation...
November 18, 2016: Development
https://www.readbyqxmd.com/read/27863372/the-fucosylated-cd147-enhances-the-autophagy-in-epithelial-ovarian-cancer-cells
#17
Zhenhua Hu, Mingbo Cai, Lu Deng, Liancheng Zhu, Jian Gao, Mingzi Tan, Juanjuan Liu, Bei Lin
Autophagy is modulated by multiple factors including CD147, but little is know about the effects and mechanism by which the modification of CD147 by Lewis y antigen regulates autophagy of ovarian cancer cell. Here, we reported that Lewis y antigen can promote basic autophagy activity and restrain autophagic cell death in ovarian cancer cells. Furthermore, human whole genome expression profile microarrays and massage pathway analysis revealed that during early stages of autophagy in ovarian cancer cells with highly expressing Lewis y antigen, PI3K/Akt-mTOR activity was reduced, in contrast, the PI3K/Akt-mTOR signaling pathway was activated as the length of amino acid deprivation increased, which inhibited eIF4G2 expression, further decreased the transcription of autophagy-related genes, suppressed autophagic cell death...
November 11, 2016: Oncotarget
https://www.readbyqxmd.com/read/27861989/a-core-function-of-eds1-with-pad4-is-to-protect-the-salicylic-acid-defense-sector-in-arabidopsis-immunity
#18
Haitao Cui, Enrico Gobbato, Barbara Kracher, Jingde Qiu, Jaqueline Bautor, Jane E Parker
Plant defenses induced by salicylic acid (SA) are vital for resistance against biotrophic pathogens. In basal and receptor-triggered immunity, SA accumulation is promoted by Enhanced Disease Susceptibility1 with its co-regulator Phytoalexin Deficient4 (EDS1/PAD4). Current models position EDS1/PAD4 upstream of SA but their functional relationship remains unclear. In a genetic and transcriptomic analysis of Arabidopsis autoimmunity caused by constitutive or conditional EDS1/PAD4 overexpression, intrinsic EDS1/PAD4 signaling properties and their relation to SA were uncovered...
November 15, 2016: New Phytologist
https://www.readbyqxmd.com/read/27861577/identifying-causal-genes-at-the-multiple-sclerosis-associated-region-6q23-using-capture-hi-c
#19
Paul Martin, Amanda McGovern, Jonathan Massey, Stefan Schoenfelder, Kate Duffus, Annie Yarwood, Anne Barton, Jane Worthington, Peter Fraser, Stephen Eyre, Gisela Orozco
BACKGROUND: The chromosomal region 6q23 has been found to be associated with multiple sclerosis (MS) predisposition through genome wide association studies (GWAS). There are four independent single nucleotide polymorphisms (SNPs) associated with MS in this region, which spans around 2.5 Mb. Most GWAS variants associated with complex traits, including these four MS associated SNPs, are non-coding and their function is currently unknown. However, GWAS variants have been found to be enriched in enhancers and there is evidence that they may be involved in transcriptional regulation of their distant target genes through long range chromatin looping...
2016: PloS One
https://www.readbyqxmd.com/read/27860235/a-functional-pseudogene-nmral2p-is-regulated-by-nrf2-and-serves-as-a-co-activator-of-nqo1-in-sulforaphane-treated-colon-cancer-cells
#20
Gavin S Johnson, Jia Li, Laura M Beaver, W Mohaiza Dashwood, Deqiang Sun, Praveen Rajendran, David E Williams, Emily Ho, Roderick H Dashwood
SCOPE: The anticancer agent sulforaphane (SFN) acts via multiple mechanisms to modulate gene expression, including the induction of nuclear factor (erythroid-derived 2)-like 2 (Nrf2)-dependent signaling and the inhibition of histone deacetylase activity. Transcriptomics studies were performed in SFN-treated human colon cancer cells and in non-transformed colonic epithelial cells in order to pursue new mechanistic leads. METHODS AND RESULTS: RNA-sequencing corroborated the expected changes in cancer-related pathways after SFN treatment...
November 18, 2016: Molecular Nutrition & Food Research
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