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https://www.readbyqxmd.com/read/27912083/robust-root-growth-in-altered-hydrotropic-response1-ahr1-mutant-of-arabidopsis-is-maintained-by-high-rate-of-cell-production-at-low-water-potential-gradient
#1
Amed Salazar-Blas, Laura Noriega-Calixto, María E Campos, Delfeena Eapen, Tania Cruz-Vázquez, Luis Castillo-Olamendi, Gabriela Sepulveda-Jiménez, Helena Porta, Joseph G Dubrovsky, Gladys I Cassab
Hydrotropism is the directional root growth response determined by water stimulus. In a water potential gradient system (WPGS) the roots of the Arabidopsis wild type have a diminished root growth compared to normal medium (NM). In contrast, the altered hydrotropic response1 (ahr1) mutant roots maintain their robust growth in the same WPGS. The aims of this work were to ascertain how ahr1 roots could sustain growth in the WPGS, with a special focus on the integration of cellular processes involved in the signaling that determines root growth during abiotic stress and their relation to hydrotropism...
November 17, 2016: Journal of Plant Physiology
https://www.readbyqxmd.com/read/27911610/successful-consecutive-expansion-of-limbal-explants-using-a-biosafe-culture-medium-under-feeder-layer-free-conditions
#2
Marina López-Paniagua, Teresa Nieto-Miguel, Ana de la Mata, Sara Galindo, José M Herreras, Rosa M Corrales, Margarita Calonge
PURPOSE: Transplantation of in vitro cultured limbal epithelial stem cells (LESCs) is a treatment widely used for LESC deficiency. However, the number of limbal tissue donors is limited, and protocols for LESC cultivation often include compounds and/or feeder layers that can induce side effects and/or increase the cost of the culture procedure. We investigated the feasibility of obtaining more than one limbal primary culture (LPC) from the same biopsy using a culture medium in which several potentially harmful compounds were replaced at the same time by biosafe supplements, allowing the LESC cultivation without feeder layers...
December 2, 2016: Current Eye Research
https://www.readbyqxmd.com/read/27908735/unr-csde1-drives-a-post-transcriptional-program-to-promote-melanoma-invasion-and-metastasis
#3
Laurence Wurth, Panagiotis Papasaikas, David Olmeda, Nadine Bley, Guadalupe T Calvo, Santiago Guerrero, Daniela Cerezo-Wallis, Javier Martinez-Useros, María García-Fernández, Stefan Hüttelmaier, Maria S Soengas, Fátima Gebauer
RNA binding proteins (RBPs) modulate cancer progression through poorly understood mechanisms. Here we show that the RBP UNR/CSDE1 is overexpressed in melanoma tumors and promotes invasion and metastasis. iCLIP sequencing, RNA sequencing, and ribosome profiling combined with in silico studies unveiled sets of pro-metastatic factors coordinately regulated by UNR as part of RNA regulons. In addition to RNA steady-state levels, UNR was found to control many of its targets at the level of translation elongation/termination...
November 14, 2016: Cancer Cell
https://www.readbyqxmd.com/read/27906160/mechanistic-insights-into-the-alternative-translation-termination-by-arfa-and-rf2
#4
Chengying Ma, Daisuke Kurita, Ningning Li, Yan Chen, Hyouta Himeno, Ning Gao
During cellular translation of mRNAs by ribosomes, various situations that would result in the pausing or stalling of translation apparatus at elongation and termination steps often occur(1-6). Except for programmed stalling, which is usually utilized by the cells to exert regulatory purposes(5,7,8), ribosomes stalled on mRNAs need to be terminated and recycled to maintain adequate cellular translation capacity(9). A large source of ribosome stalling originates in aberrant mRNAs that lack a stop codon. Transcriptional errors and misprocessing of primary transcripts, as well as undesired mRNA cleavage, all contribute to the formation of non-stop mRNAs...
December 1, 2016: Nature
https://www.readbyqxmd.com/read/27899647/spliceosomal-protein-eftud2-mutation-leads-to-p53-dependent-apoptosis-in-zebrafish-neural-progenitors
#5
Lei Lei, Shou-Yu Yan, Ran Yang, Jia-Yu Chen, Yumei Li, Ye Bu, Nannan Chang, Qinchao Zhou, Xiaojun Zhu, Chuan-Yun Li, Jing-Wei Xiong
Haploinsufficiency of EFTUD2 (Elongation Factor Tu GTP Binding Domain Containing 2) is linked to human mandibulofacial dysostosis, Guion-Almeida type (MFDGA), but the underlying cellular and molecular mechanisms remain to be addressed. We report here the isolation, cloning and functional analysis of the mutated eftud2 (snu114) in a novel neuronal mutant fn10a in zebrafish. This mutant displayed abnormal brain development with evident neuronal apoptosis while the development of other organs appeared less affected...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899640/structural-insights-into-nusg-regulating-transcription-elongation
#6
Bin Liu, Thomas A Steitz
NusG is an essential transcription factor that plays multiple key regulatory roles in transcription elongation, termination and coupling translation and transcription. The core role of NusG is to enhance transcription elongation and RNA polymerase processivity. Here, we present the structure of Escherichia coli RNA polymerase complexed with NusG. The structure shows that the NusG N-terminal domain (NGN) binds at the central cleft of RNA polymerase surrounded by the β' clamp helices, the β protrusion, and the β lobe domains to close the promoter DNA binding channel and constrain the β' clamp domain, but with an orientation that is different from the one observed in the archaeal β' clamp-Spt4/5 complex...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899597/thermotoga-maritima-nusg-domain-interaction-mediates-autoinhibition-and-thermostability
#7
Johanna Drögemüller, Christin Schneider, Kristian Schweimer, Martin Strauß, Birgitta M Wöhrl, Paul Rösch, Stefan H Knauer
NusG, the only universally conserved transcription factor, comprises an N- and a C-terminal domain (NTD, CTD) that are flexibly connected and move independently in Escherichia coli and other organisms. In NusG from the hyperthermophilic bacterium Thermotoga maritima (tmNusG), however, NTD and CTD interact tightly. This closed state stabilizes the CTD, but masks the binding sites for the interaction partners Rho, NusE and RNA polymerase (RNAP), suggesting that tmNusG is autoinhibited. Furthermore, tmNusG and some other bacterial NusGs have an additional domain, DII, of unknown function...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898830/endoplasmic-reticulum-body-related-gene-expression-in-different-root-zones-of-arabidopsis-isolated-by-laser-assisted-microdissection
#8
Maxime Gotté, Magalie Bénard, Marie-Christine Kiefer-Meyer, Rim Jaber, John P Moore, Maïté Vicré-Gibouin, Azeddine Driouich
Endoplasmic reticulum (ER) bodies are important organelles for root defense. However, little is known regarding the genetic control of their formation in root tissues. In the present study, (L.) Heynh. roots were dissected using laser-assisted microdissection (LAM) with minimal sample preparation (no fixation or embedding steps) and the expression of genes associated with ER body formation and function was assessed by real-time quantitative reverse-transcription polymerase chain reaction (RT-qRT-PCR) in the presence and absence of the defense phytohormone methyl jasmonate (MeJA)...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27895724/expression-profile-of-spaca5-spaca5-in-spermatogenesis-and-transitional-cell-carcinoma-of-the-bladder
#9
Xiao-Yue Zhang, Qiu-Xia Yan, Xiao-Yan Guo, Cai-Rong Chen, Run-Qiang Chen, Zhi-Ming Cai, Ai-Fa Tang
The majority of bladder cancer-associated mortalities are due to transitional cell carcinoma (TCC), which is the most prevalent and chemoresistant malignancy of the bladder. Sperm acrosome associated 5 (SPACA5)/Spaca5 is a sperm acrosome-associated, c-type lysozyme-like protein that has been recently identified, and has been designated as an attractive candidate antigen for cancer testis. In the present study, the expression profile of SPACA5/Spaca5 was analyzed in spermatogenesis and TCC of the bladder using diverse molecular and cellular biology methods...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27892458/modulation-of-mrna-and-lncrna-expression-dynamics-by-the-set2-rpd3s-pathway
#10
Ji Hyun Kim, Bo Bae Lee, Young Mi Oh, Chenchen Zhu, Lars M Steinmetz, Yookyeong Lee, Wan Kyu Kim, Sung Bae Lee, Stephen Buratowski, TaeSoo Kim
H3K36 methylation by Set2 targets Rpd3S histone deacetylase to transcribed regions of mRNA genes, repressing internal cryptic promoters and slowing elongation. Here we explore the function of this pathway by analysing transcription in yeast undergoing a series of carbon source shifts. Approximately 80 mRNA genes show increased induction upon SET2 deletion. A majority of these promoters have overlapping lncRNA transcription that targets H3K36me3 and deacetylation by Rpd3S to the mRNA promoter. We previously reported a similar mechanism for H3K4me2-mediated repression via recruitment of the Set3C histone deacetylase...
November 28, 2016: Nature Communications
https://www.readbyqxmd.com/read/27890635/hos1-facilitates-the-phytochrome-b-mediated-inhibition-of-pif4-function-during-hypocotyl-growth-in-arabidopsis
#11
Ju-Heon Kim, Hyo-Jun Lee, Jae-Hoon Jung, Sangmin Lee, Chung-Mo Park
Upon exposure to light, developing seedlings undergo photomorphogenesis, as illustrated by inhibition of hypocotyl elongation, cotyledon opening, and leaf greening. Hypocotyl growth is a well-established model for photomorphogenesis studies. During hypocotyl photomorphogenesis, light signals are sensed by multiple photoreceptors, among which the red/far-red light-sensing phytochromes have been extensively studied. However, it is not fully understood how the phytochromes modulate hypocotyl growth. Here, we demonstrated that HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1 (HOS1), which is known to either act as E3 ubiquitin ligase or affect chromatin organization, inhibits the transcriptional activation activity of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) that promotes hypocotyl growth...
November 24, 2016: Molecular Plant
https://www.readbyqxmd.com/read/27889523/identification-of-target-genes-and-processes-involved-in-erucic-acid-accumulation-during-seed-development-in-the-biodiesel-feedstock-pennycress-thlaspi-arvense-l
#12
Ana Claver, Raquel Rey, M Victoria López, Rafael Picorel, Miguel Alfonso
We studied erucic acid accumulation in the biodiesel feedstock Pennycress (Thlaspi arvense L.) as a first step towards the development of a sustainable strategy for biofuel production in the EU territory. To that end, two inbred Pennycress lines of European origin, "NASC" and "French," were cultivated in a controlled chamber and in experimental field plots, and their growth, seed production and seed oil characteristics analyzed. Differences in some agronomical traits like vernalization (winter-French versus spring-NASC), flowering time (delayed in the French line) and seed production (higher in the French line) were detected...
November 18, 2016: Journal of Plant Physiology
https://www.readbyqxmd.com/read/27889295/novel-t7-like-expression-systems-used-for-halomonas
#13
Han Zhao, Haoqian M Zhang, Xiangbin Chen, Teng Li, Qiong Wu, Qi Ouyang, Guo-Qiang Chen
To engineer non-model organisms, suitable genetic parts must be available. However, biological parts are often host strain sensitive. It is therefore necessary to develop genetic parts that are functional regardless of host strains. Here we report several novel phage-derived expression systems used for transcriptional control in non-model bacteria. Novel T7-like RNA polymerase-promoter pairs were obtained by mining phage genomes, followed by in vivo characterization in non-model strains Halomonas spp TD01 and Pseudomonas entomophila...
November 24, 2016: Metabolic Engineering
https://www.readbyqxmd.com/read/27889265/integration-of-phytochrome-and-cryptochrome-signals-determines-plant-growth-during-competition-for-light
#14
Mieke de Wit, Diederik H Keuskamp, Franca J Bongers, Patricia Hornitschek, Charlotte M M Gommers, Emilie Reinen, Carmen Martínez-Cerón, Christian Fankhauser, Ronald Pierik
Plants in dense vegetation perceive their neighbors primarily through changes in light quality. Initially, the ratio between red (R) and far-red (FR) light decreases due to reflection of FR by plant tissue well before shading occurs. Perception of low R:FR by the phytochrome photoreceptors induces the shade avoidance response [1], of which accelerated elongation growth of leaf-bearing organs is an important feature. Low R:FR-induced phytochrome inactivation leads to the accumulation and activation of the transcription factors PHYTOCHROME-INTERACTING FACTORs (PIFs) 4, 5, and 7 and subsequent expression of their growth-mediating targets [2, 3]...
November 17, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/27888523/the-cotton-%C3%AE-galactosyltransferase-1-galt1-that-galactosylates-arabinogalactan-proteins-participates-in-controlling-fiber-development
#15
Li-Xia Qin, Yun Chen, Wei Zeng, Yang Li, Lu Gao, Deng-Di Li, Antony Bacic, Wen-Liang Xu, Xue-Bao Li
Arabinogalactan-proteins (AGPs) are highly glycosylated proteins which play pivotal roles in diverse developmental processes in plants. Type II AG glycans, mostly O-linked to the hydroxyproline residues of the protein backbone, account for up to 95% w/w of the AGP, but their functions are still largely unclear. Cotton fibers are extremely elongated single-cell trichomes on the seed epidermis. However, little is known of the molecular basis governing the regulation of fiber cell development. Here, we characterized the role of a CAZy glycosyltransferase (GT) family 31 member GhGalT1 in cotton fiber development...
November 26, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27882920/repression-of-rna-polymerase-by-the-archaeo-viral-regulator-orf145-rip
#16
Carol Sheppard, Fabian Blombach, Adam Belsom, Sarah Schulz, Tina Daviter, Katherine Smollett, Emilie Mahieu, Susanne Erdmann, Philip Tinnefeld, Roger Garrett, Dina Grohmann, Juri Rappsilber, Finn Werner
Little is known about how archaeal viruses perturb the transcription machinery of their hosts. Here we provide the first example of an archaeo-viral transcription factor that directly targets the host RNA polymerase (RNAP) and efficiently represses its activity. ORF145 from the temperate Acidianus two-tailed virus (ATV) forms a high-affinity complex with RNAP by binding inside the DNA-binding channel where it locks the flexible RNAP clamp in one position. This counteracts the formation of transcription pre-initiation complexes in vitro and represses abortive and productive transcription initiation, as well as elongation...
November 24, 2016: Nature Communications
https://www.readbyqxmd.com/read/27882317/bacterial-rna-polymerase-dna-interaction-the-driving-force-of-gene-expression-and-the-target-for-drug-action
#17
REVIEW
Jookyung Lee, Sergei Borukhov
DNA-dependent multisubunit RNA polymerase (RNAP) is the key enzyme of gene expression and a target of regulation in all kingdoms of life. It is a complex multifunctional molecular machine which, unlike other DNA-binding proteins, engages in extensive and dynamic interactions (both specific and nonspecific) with DNA, and maintains them over a distance. These interactions are controlled by DNA sequences, DNA topology, and a host of regulatory factors. Here, we summarize key recent structural and biochemical studies that elucidate the fine details of RNAP-DNA interactions during initiation...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27879391/rice-leaf-angle-and-grain-size-are-affected-by-the-osbul1-transcriptional-activator-complex
#18
Seonghoe Jang, Gynheung An, Hsing-Yi Li
Rice atypical HLH protein Oryza sativa BRASSINOSTEROID UPREGULATED 1-LIKE 1 (OsBUL1) is preferentially expressed in the laminar joint where it controls cell elongation and positively affects leaf angles. OsBUL1 knockout mutant (osbul1) and transgenic rice for double stranded RNA interference (dsRNAi) of OsBUL1 produced erected leaves with smaller grains whereas OsBUL1 overexpressors and an activation tagging line of OsBUL1 exhibited increased laminar inclination and grain size. Moreover, OsBUL1 expression was induced by brassinolide (BL) and osbul1 did not respond to BL treatment...
November 22, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27879331/brd4-activates-early-viral-transcription-upon-human-papillomavirus-18-infection-of-primary-keratinocytes
#19
Caleb C McKinney, Min Jung Kim, Dan Chen, Alison A McBride
: Human papillomaviruses (HPVs) replicate in the cutaneous and mucosal epithelia, and the infectious cycle is synchronous with the differentiation program of the host keratinocytes. The virus initially infects dividing cells in the lower layers of the epithelium, where it establishes a persistent infection. The viral genome is maintained as a low-copy-number, extrachromosomal element in these proliferating cells but switches to the late stage of the life cycle in differentiated cells...
November 22, 2016: MBio
https://www.readbyqxmd.com/read/27876642/arabidopsis-nf-ycs-mediate-the-light-control-of-hypocotyl-elongation-via-modulating-histone-acetylation
#20
Yang Tang, Xuncheng Liu, Xu Liu, Yuge Li, Keqiang Wu, Xingliang Hou
Light is a crucial environmental signal that promotes photomorphogenesis, the developmental process containing a series of light-dependent alterations for plants to adapt various external challenges. Chromatin modification has been proposed to be involved in such light-mediated growth, but the underlying mechanism is still elusive. Here, we identify that the four Arabidopsis thaliana Nuclear Factor-YC homologues NF-YC1, NF-YC3, NF-YC4, and NF-YC9 (NF-YCs) function redundantly as the repressors of light control of hypocotyl elongation via histone de-acetylation...
November 19, 2016: Molecular Plant
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