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https://www.readbyqxmd.com/read/27933319/a-metabolic-widget-adjusts-the-phosphoenolpyruvate-dependent-fructose-influx-in-pseudomonas-putida
#1
Max Chavarría, Ángel Goñi-Moreno, Víctor de Lorenzo, Pablo I Nikel
Fructose uptake in the soil bacterium Pseudomonas putida occurs through a canonical phosphoenolpyruvate (PEP)-dependent sugar transport system (PTS(Fru)). The logic of the genetic circuit that rules its functioning is puzzling: the transcription of the fruBKA operon, encoding all the components of PTS(Fru), can escape the repression exerted by the catabolite repressor/activator protein Cra solely in the presence of intracellular fructose-1-P, an agonist formed only when fructose has been already transported...
November 2016: MSystems
https://www.readbyqxmd.com/read/27933070/transcriptional-responses-in-root-and-leaf-of-prunus-persica-under-drought-stress-using-rna-sequencing
#2
Najla Ksouri, Sergio Jiménez, Christina E Wells, Bruno Contreras-Moreira, Yolanda Gogorcena
Prunus persica L. Batsch, or peach, is one of the most important crops and it is widely established in irrigated arid and semi-arid regions. However, due to variations in the climate and the increased aridity, drought has become a major constraint, causing crop losses worldwide. The use of drought-tolerant rootstocks in modern fruit production appears to be a useful method of alleviating water deficit problems. However, the transcriptomic variation and the major molecular mechanisms that underlie the adaptation of drought-tolerant rootstocks to water shortage remain unclear...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27933063/aire-downregulation-is-associated-with-changes-in-the-posttranscriptional-control-of-peripheral-tissue-antigens-in-medullary-thymic-epithelial-cells
#3
Ernna H Oliveira, Claudia Macedo, Cristhianna V Collares, Ana Carolina Freitas, Paula Barbim Donate, Elza T Sakamoto-Hojo, Eduardo A Donadi, Geraldo A Passos
Autoimmune regulator (Aire) is a transcriptional regulator of peripheral tissue antigens (PTAs) and microRNAs (miRNAs) in medullary thymic epithelial cells (mTECs). In this study, we tested the hypothesis that Aire also played a role as an upstream posttranscriptional controller in these cells and that variation in its expression might be associated with changes in the interactions between miRNAs and the mRNAs encoding PTAs. We demonstrated that downregulation of Aire in vivo in the thymuses of BALB/c mice imbalanced the large-scale expression of these two RNA species and consequently their interactions...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27933036/functional-analysis-of-the-nitrogen-metabolite-repression-regulator-gene-nmra-in-aspergillus-flavus
#4
Xiaoyun Han, Mengguang Qiu, Bin Wang, Wen-Bing Yin, Xinyi Nie, Qiuping Qin, Silin Ren, Kunlong Yang, Feng Zhang, Zhenhong Zhuang, Shihua Wang
In Aspergillus nidulans, the nitrogen metabolite repression (NMR) regulator NmrA plays a major role in regulating the activity of the GATA transcription factor AreA during nitrogen metabolism. However, the function of nmrA in A. flavus has not been previously studied. Here, we report the identification and functional analysis of nmrA in A. flavus. Our work showed that the amino acid sequences of NmrA are highly conserved among Aspergillus species and that A. flavus NmrA protein contains a canonical Rossmann fold motif...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27932543/members-of-the-zinc-cluster-factor-family-alters-virulence-in-candida-albicans
#5
Luca Issi, Rhys A Farrer, Kelly Pastor, Benjamin Landry, Toni Delorey, George W Bell, Dawn A Thompson, Christina A Cuomo, Reeta P Rao
Virtually all humans are colonized with Candida albicans However, in immunocompromised individuals this benign commensal organism becomes a serious, life-threatening pathogen. Here, we describe and analyze the regulatory networks that modulate innate responses in the host niches. We identified Zcf15 and Zcf29, two Zinc Cluster transcription Factors (ZCF) that are required for C. albicans virulence. Previous sequence analysis of clinical C. albicans isolates from immunocompromised patients indicates that both ZCF genes diverged during clonal evolution...
December 7, 2016: Genetics
https://www.readbyqxmd.com/read/27932421/myb89-transcription-factor-represses-seed-oil-accumulation
#6
Dong Li, Changyu Jin, Shaowei Duan, Yana Zhu, Shuanghui Qi, Kaige Liu, Chenhao Gao, Haoli Ma, Meng Zhang, Yuncheng Liao, Mingxun Chen
In many higher plants, seed oil accumulation is precisely controlled by intricate multi-level regulatory networks, among which transcriptional regulation mainly influences oil biosynthesis. In Arabidopsis, the master positive transcription factors, WRINKLED1 (WRI1) and LEAFY COTYLEDON1-LIKE (L1L), are important for seed oil accumulation. We found that an R2R3-MYB transcription factor, MYB89, was predominantly expressed in developing seeds during maturation. Oil and major fatty acid biosynthesis in seeds was significantly promoted by myb89-1 mutation and MYB89 knockdown; MYB89 was thus an important repressor during seed oil accumulation...
December 8, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27932399/novel-hybrid-phenotype-revealed-in-small-cell-lung-cancer-by-a-transcription-factor-network-model-that-can-explain-tumor-heterogeneity
#7
Akshata R Udyavar, David J Wooten, Megan D Hoeksema, Mukesh Bansal, Andrea Califano, Lourdes Estrada, Santiago Schnell, Jonathan M Irish, Pierre P Massion, Vito Quaranta
Small cell lung cancer (SCLC) is a devastating disease due to its propensity for early invasion and refractory relapse after initial treatment response. Although these aggressive traits have been associated with phenotypic heterogeneity, our understanding of this association remains incomplete. To fill this knowledge gap, we inferred a set of 33 transcription factors (TF) associated with gene signatures of the known neuroendocrine/epithelial (NE) and non-neuroendocrine/mesenchymal-like (ML) SCLC phenotypes...
December 8, 2016: Cancer Research
https://www.readbyqxmd.com/read/27930885/robust-synthetic-circuits-for-two-dimensional-control-of-gene-expression-in-yeast
#8
Andres Aranda-Diaz, Kieran Mace, Ignacio Zuleta, Patrick Harrigan, Hana El-Samad
Cellular phenotypes are the result of complex interactions between many components. Understanding and predicting the system level properties of the resulting networks requires the development of perturbation tools that can simultaneously and independently modulate multiple cellular variables. Here, we develop synthetic modules that use different arrangements of two transcriptional regulators to achieve either concurrent and independent control of the expression of two genes, or decoupled control of the mean and variance of a single gene...
December 8, 2016: ACS Synthetic Biology
https://www.readbyqxmd.com/read/27930681/transcriptomic-changes-in-liver-of-young-bulls-caused-by-diets-low-in-mineral-and-protein-contents-and-supplemented-with-n-3-fatty-acids-and-conjugated-linoleic-acid
#9
Sara Pegolo, Alessio Cecchinato, Núria Mach, Massimiliano Babbucci, Marianna Pauletto, Luca Bargelloni, Stefano Schiavon, Giovanni Bittante
The aim of the present study was to identify transcriptional modifications and regulatory networks accounting for physiological and metabolic responses to specific nutrients in the liver of young Belgian Blue × Holstein bulls using RNA-sequencing. A larger trial has been carried out in which animals were fed with different diets: 1] a conventional diet; 2] a low-protein/low-mineral diet (low-impact diet) and 3] a diet enriched in n-3 fatty acids (FAs), conjugated linoleic acid (CLA) and vitamin E (nutraceutical diet)...
2016: PloS One
https://www.readbyqxmd.com/read/27930646/retinal-expression-of-the-drosophila-eyes-absent-gene-is-controlled-by-several-cooperatively-acting-cis-regulatory-elements
#10
Bonnie M Weasner, Brandon P Weasner, Sarah D Neuman, Arash Bashirullah, Justin P Kumar
The eyes absent (eya) gene of the fruit fly, Drosophila melanogaster, is a member of an evolutionarily conserved gene regulatory network that controls eye formation in all seeing animals. The loss of eya leads to the complete elimination of the compound eye while forced expression of eya in non-retinal tissues is sufficient to induce ectopic eye formation. Within the developing retina eya is expressed in a dynamic pattern and is involved in tissue specification/determination, cell proliferation, apoptosis, and cell fate choice...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27930301/reprogramming-cell-fate-with-a-genome-scale-library-of-artificial-transcription-factors
#11
Asuka Eguchi, Matthew J Wleklinski, Mackenzie C Spurgat, Evan A Heiderscheit, Anna S Kropornicka, Catherine K Vu, Devesh Bhimsaria, Scott A Swanson, Ron Stewart, Parameswaran Ramanathan, Timothy J Kamp, Igor Slukvin, James A Thomson, James R Dutton, Aseem Z Ansari
Artificial transcription factors (ATFs) are precision-tailored molecules designed to bind DNA and regulate transcription in a preprogrammed manner. Libraries of ATFs enable the high-throughput screening of gene networks that trigger cell fate decisions or phenotypic changes. We developed a genome-scale library of ATFs that display an engineered interaction domain (ID) to enable cooperative assembly and synergistic gene expression at targeted sites. We used this ATF library to screen for key regulators of the pluripotency network and discovered three combinations of ATFs capable of inducing pluripotency without exogenous expression of Oct4 (POU domain, class 5, TF 1)...
December 5, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27930300/an-nad-dependent-transcriptional-program-governs-self-renewal-and-radiation-resistance-in-glioblastoma
#12
Amit D Gujar, Son Le, Diane D Mao, David Y A Dadey, Alice Turski, Yo Sasaki, Diane Aum, Jingqin Luo, Sonika Dahiya, Liya Yuan, Keith M Rich, Jeffrey Milbrandt, Dennis E Hallahan, Hiroko Yano, David D Tran, Albert H Kim
Accumulating evidence suggests cancer cells exhibit a dependency on metabolic pathways regulated by nicotinamide adenine dinucleotide (NAD(+)). Nevertheless, how the regulation of this metabolic cofactor interfaces with signal transduction networks remains poorly understood in glioblastoma. Here, we report nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting step in NAD(+) synthesis, is highly expressed in glioblastoma tumors and patient-derived glioblastoma stem-like cells (GSCs). High NAMPT expression in tumors correlates with decreased patient survival...
December 7, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27929739/timing-of-dna-lesion-recognition-ubiquitin-signalling-in-the-ner-pathway
#13
Shalaka Chitale, Holger Richly
Damaged DNA is repaired by specialized repair factors that are recruited in a well-orchestrated manner to the damage site. The DNA damage response at UV inflicted DNA lesions is accompanied by posttranslational modifications of DNA repair factors and the chromatin environment sourrounding the lesion. In particular, mono- and poly-ubiquitylation events are an integral part of the DNA damage signalling. Whereas ubiquitin signalling at DNA doublestrand breaks has been subject to intensive studies comparatively little is known about the intricacies of ubiquitylation events occuring during nucleotide excision repair (NER), the major pathway to remove bulky helix lesions...
December 8, 2016: Cell Cycle
https://www.readbyqxmd.com/read/27929373/tumor-induced-mdsc-act-via-remote-control-to-inhibit-l-selectin-dependent-adaptive-immunity-in-lymph-nodes
#14
Amy W Ku, Jason B Muhitch, Colin A Powers, Michael G Diehl, Minhyung Kim, Daniel T Fisher, Anand P Sharda, Virginia K Clements, Kieran O'Loughlin, Hans Minderman, Michelle N Messmer, Jing Ma, Joseph J Skitzki, Douglas A Steeber, Bruce Walcheck, Suzanne Ostrand-Rosenberg, Scott I Abrams, Sharon S Evans
Myeloid-derived suppressor cells (MDSC) contribute to an immunosuppressive network that drives cancer escape by disabling T cell adaptive immunity. The prevailing view is that MDSC-mediated immunosuppression is restricted to tissues where MDSC co-mingle with T cells. Here we show that splenic or, unexpectedly, blood-borne MDSC execute far-reaching immune suppression by reducing expression of the L-selectin lymph node (LN) homing receptor on naïve T and B cells. MDSC-induced L-selectin loss occurs through a contact-dependent, post-transcriptional mechanism that is independent of the major L-selectin sheddase, ADAM17, but results in significant elevation of circulating L-selectin in tumor-bearing mice...
December 8, 2016: ELife
https://www.readbyqxmd.com/read/27927271/long-noncoding-rna-expression-signatures-of-abdominal-aortic-aneurysm-revealed-by-microarray
#15
Yao Guo Yang, Mei Xia Li, Lei Kou, You Zhou, Yan Wen Qin, Xiao Jun Liu, Zhong Chen
OBJECTIVE: This study is aimed at observing the role of long noncoding RNAs (lncRNAs) in the pathogenesis of abdominal aortic aneurysm (AAA). METHODS: LncRNA and mRNA expression signatures of AAA tissues and normal abdominal aortic tissues (NT) were analyzed by microarray and further verified by Real-time quantitative reverse-transcription PCR (qRT-PCR). The lncRNAs-mRNAs targeting relationships were identified using computational analysis. The effect of lnc-ARG on 5-lipoxygenase (ALOX5) expression was tested in HeLa cells...
October 2016: Biomedical and Environmental Sciences: BES
https://www.readbyqxmd.com/read/27925216/light-regulation-of-alternative-pre-mrna-splicing-in-plants
#16
Hangxiao Zhang, Chentao Lin, Lianfeng Gu
Alternative splicing (AS) is a major post-transcriptional mechanism to enhance the diversity of proteome in response to environmental signals. Among the numerous external signals perceived by plants, light is the most crucial one. Plants utilize complex photoreceptor signaling networks to sense different light conditions and adjust their growth and development accordingly. Although light-mediated gene expression has been widely investigated, little is known regarding the mechanism of light affecting AS to modulate mRNA at the post-transcriptional level...
December 7, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27924555/how-genetics-has-helped-piece-together-the-mapk-signaling-pathway
#17
Dariel Ashton-Beaucage, Marc Therrien
Cells respond to changes in their environment, to developmental cues, and to pathogen aggression through the action of a complex network of proteins. These networks can be decomposed into a multitude of signaling pathways that relay signals from the microenvironment to the cellular components involved in eliciting a specific response. Perturbations in these signaling processes are at the root of multiple pathologies, the most notable of these being cancer. The study of receptor tyrosine kinase (RTK) signaling led to the first description of a mechanism whereby an extracellular signal is transmitted to the nucleus to induce a transcriptional response...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924512/computational-analysis-reveals-microrna-mrna-regulatory-network-in-esophageal-squamous-cell-carcinoma
#18
Jie Zhao, Bi-Cheng Zhang, Li-Fang Yu, Wei-Xing Wang, Yong Zhao, Zhi-Guo Rao
MicroRNAs (miRNAs) are known to regulate post-transcriptional gene expression. They are involved in carcinogenesis and tumor progression. The aim of this study was to explore the microRNA-mRNA regulatory network in esophageal squamous cell carcinoma (ESCC) using comprehensive computational approaches. In this study we have selected a total of 11 miRNAs from one previously reported study in ESCC. The mRNA targets of these miRNAs were predicted using various algorithms. The expression profiles of these mRNA targets were identified on DNA microarray experiment dataset across ESCC tissue samples...
December 2016: Journal of Huazhong University of Science and Technology. Medical Sciences
https://www.readbyqxmd.com/read/27924190/network-analysis-of-human-post-mortem-microarrays-reveals-novel-genes-micrornas-and-mechanistic-scenarios-of-potential-importance-in-fighting-huntington-s-disease
#19
Sreedevi Chandrasekaran, Danail Bonchev
Huntington's disease is a progressive neurodegenerative disorder characterized by motor disturbances, cognitive decline, and neuropsychiatric symptoms. In this study, we utilized network-based analysis in an attempt to explore and understand the underlying molecular mechanism and to identify critical molecular players of this disease condition. Using human post-mortem microarrays from three brain regions (cerebellum, frontal cortex and caudate nucleus) we selected in a four-step procedure a seed set of highly modulated genes...
2016: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27924063/%C3%AE-np63%C3%AE-and-micrornas-leveraging-the-epithelial-mesenchymal-transition
#20
REVIEW
Andrew J Stacy, Michael P Craig, Suraj Sakaram, Madhavi Kadakia
The epithelial-mesenchymal transition (EMT) is a cellular reprogramming mechanism that is an underlying cause of cancer metastasis. Recent investigations have uncovered an intricate network of regulation involving the TGFβ, Wnt, and Notch signaling pathways and small regulatory RNA species called microRNAs (miRNAs). The activity of a transcription factor vital to the maintenance of epithelial stemness, ΔNp63α, has been shown to modulate the activity of these EMT pathways to either repress or promote EMT...
December 4, 2016: Oncotarget
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