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a cis-acting acting element in the promoter

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https://www.readbyqxmd.com/read/28729874/systematic-analysis-of-hsf-family-genes-in-the-brassica-napus-genome-reveals-novel-responses-to-heat-drought-and-high-co2-stresses
#1
Xiaoyi Zhu, Chunqian Huang, Liang Zhang, Hongfang Liu, Jinhui Yu, Zhiyong Hu, Wei Hua
Drought and heat stress are major causes of lost plant crop yield. In the future, high levels of CO2, in combination of other abiotic stress factors, will become a novel source of stress. Little is known of the mechanisms involved in the acclimation responses of plants to this combination of abiotic stress factors, though it has been demonstrated that heat shock transcription factors (Hsfs) are involved in plant response to various abiotic stresses. In this study, we performed a genome-wide identification and a systematic analysis of genes in the Hsf gene family in Brassica napus...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28726715/overexpression-of-the-osimp-gene-increases-the-accumulation-of-inositol-and-confers-enhanced-cold-tolerance-in-tobacco-through-modulation-of-the-antioxidant-enzymes-activities
#2
Rong-Xiang Zhang, Li-Jun Qin, De-Gang Zhao
Inositol is a cyclic polyol that is involved in various physiological processes, including signal transduction and stress adaptation in plants. l-myo-inositol monophosphatase (IMPase) is one of the metal-dependent phosphatase family members and catalyzes the last reaction step of biosynthesis of inositol. Although increased IMPase activity induced by abiotic stress has been reported in chickpea plants, the role and regulation of the IMP gene in rice (Oryza sativa L.) remains poorly understood. In the present work, we obtained a full-length cDNA sequence coding IMPase in the cold tolerant rice landraces in Gaogonggui, which is named as OsIMP...
July 20, 2017: Genes
https://www.readbyqxmd.com/read/28726630/dissection-of-specific-binding-of-hiv-1-gag-to-the-packaging-signal-in-viral-rna
#3
Mauricio Comas-Garcia, Siddhartha Ak Datta, Laura Baker, Rajat Varma, Prabhakar R Gudla, Alan Rein
Selective packaging of HIV-1 genomic RNA (gRNA) requires the presence of a cis-acting RNA element called the "packaging signal" (Ψ). However, the mechanism by which Ψ promotes selective packaging of the gRNA is not well understood. We used fluorescence correlation spectroscopy and quenching data to monitor the binding of recombinant HIV-1 Gag protein to Cy5-tagged 190-base RNAs. At physiological ionic strength, Gag binds with very similar, nanomolar affinities to both Ψ-containing and control RNAs. We challenged these interactions by adding excess competing tRNA; introducing mutations in Gag; or raising the ionic strength...
July 20, 2017: ELife
https://www.readbyqxmd.com/read/28693485/three-members-of-medicago-truncatula-st-family-are-ubiquitous-during-development-and-modulated-by-nutritional-status-mtst1-and-dehydration-mtst2-and-mtst3
#4
Lucía Albornos, Ignacio Martín, Emilia Labrador, Berta Dopico
BACKGROUND: ShooT specific/Specific Tissue (ST) belong to a protein family of unknown function characterized by the DUF2775 domain and produced in specific taxonomic plant families, mainly Fabaceae and Asteraceae, with the Medicago truncatula ST family being the largest. The putative roles proposed for this family are cell elongation, biotic interactions, abiotic stress and N reserve. The aim of this work was to go deeper into the role of three M. truncatula ST proteins, namely ST1, ST2 and ST3...
July 10, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28691155/construction-of-a-novel-synthetic-root-specific-promoter-and-its-characterization-in-transgenic-tobacco-plants
#5
Chakravarthi Mohan, Ashwin Narayan Jayanarayanan, Subramonian Narayanan
Synthetic promoter technology offers a framework for designing expression cassettes that could provide precise control of transgene expression. Such artificially designed promoters enable defined transgene regulation, reduce unwanted background expression, and can overcome homology-dependent gene silencing in transgenic plants. In the present study, a synthetic root-specific module was designed using characterized cis-acting elements, fused with minimal promoter (86 bp) from PortUbi882 promoter, and cloned in pCAMBIA1305...
August 2017: 3 Biotech
https://www.readbyqxmd.com/read/28676446/identification-and-expression-profiling-of-oryza-sativa-nucleotidyl-transferase-protein-ntp-genes-under-various-stress-conditions
#6
Haiqi Yang, Jianbo Song, Luming Yue, Xiaowei Mo, Jun Song, Beixin Mo
Nucleotidyl transferase proteins (NTPs) modify the 3' ends of mature small RNAs, leading to their stabilization or degradation. The first two plant NTPs, HESO1 and URT1, were identified in Arabidopsis. These two NTPs act cooperatively to uridylate the 3' terminal nucleotide of specific miRNAs, leading to their degradation and thereby affecting the expression of genes regulated by these miRNAs. Little is known about NTPs in other plants. Here, we performed a comprehensive analysis of 13 putative NTP genes in Oryza sativa, a major crop in global food production...
July 1, 2017: Gene
https://www.readbyqxmd.com/read/28673963/yeast-pah1-encoded-phosphatidate-phosphatase-controls-the-expression-of-cho1-encoded-phosphatidylserine-synthase-for-membrane-phospholipid-synthesis
#7
Gil-Soo Han, George M Carman
The PAH1-encoded phosphatidate phosphatase (PAP), which catalyzes the committed step for the synthesis of triacylglycerol in Saccharomyces cerevisiae, exerts a negative regulatory effect on the level of phosphatidate used for the de novo synthesis of membrane phospholipids. This raises the question whether PAP thereby affects the expression and activity of enzymes involved in phospholipid synthesis. Here, we examined the PAP-mediated regulation of CHO1-encoded phosphatidylserine synthase (PSS), which catalyzes the committed step for the synthesis of major phospholipids via the CDP-diacylglycerol pathway...
July 3, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28659964/transcription-factor-repertoire-of-necrotrophic-fungal-phytopathogen-ascochyta-rabiei-predominance-of-myb-transcription-factors-as-potential-regulators-of-secretome
#8
Sandhya Verma, Rajesh K Gazara, Praveen K Verma
Transcription factors (TFs) are the key players in gene expression and their study is highly significant for shedding light on the molecular mechanisms and evolutionary history of organisms. During host-pathogen interaction, extensive reprogramming of gene expression facilitated by TFs is likely to occur in both host and pathogen. To date, the knowledge about TF repertoire in filamentous fungi is in infancy. The necrotrophic fungus Ascochyta rabiei, that causes destructive Ascochyta blight (AB) disease of chickpea (Cicer arietinum), demands more comprehensive study for better understanding of Ascochyta-legume pathosystem...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28647924/comparative-expression-analysis-of-rice-and-arabidopsis-peroxiredoxin-genes-suggests-conserved-or-diversified-roles-between-the-two-species-and-leads-to-the-identification-of-tandemly-duplicated-rice-peroxiredoxin-genes-differentially-expressed-in-seeds
#9
Yun-Shil Gho, Sun-A Park, Sung-Ruyl Kim, Anil Kumar Nalini Chandran, Gynheung An, Ki-Hong Jung
BACKGROUND: Peroxiredoxins (PRXs) have recently been identified as plant antioxidants. Completion of various genome sequencing projects has provided genome-wide information about PRX genes in major plant species. Two of these -- Oryza sativa (rice) and Arabidopsis -- each have 10 PRX members. Although significant progress has been made in understanding their biological roles in Arabidopsis, those functions in rice, a model crop plant, have not been well studied. RESULTS: We performed a comparative expression analysis of rice and Arabidopsis PRXs...
December 2017: Rice
https://www.readbyqxmd.com/read/28642136/a-novel-hepatitis-b-virus-derived-cis-acting-sequence-that-enhances-expression-of-transgenes-delivered-by-plasmid-vectors-in-eukaryote-cell-culture-systems
#10
Seoung-Ae Lee, Hong Kim, So-Young Lee, Bum-Joon Kim
We tested the effectiveness of a novel 13-bp hepatitis B virus (HBV)-derived cis-acting element (CAE) (ACCTCGACAAGGC), called the DT2 CAE, in augmenting transgene expression delivered by plasmid vectors in eukaryotic cells. The addition of the DT2 CAE just upstream of the start codon of several different target proteins (luciferase, EGFP, LHB, HBsAg, and MIF) in DNA plasmid constructs enhanced their translation in a posttranscriptional manner, irrespective of cell type (cell lines or primary cells) or promoter (CMV or HBV preS1 promoters), suggesting its feasibility for enhanced protein production in eukaryotic cell systems...
June 19, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28636266/marap2-4-a-waterlogging-responsive-erf-from-mentha-regulates-bidirectional-sugar-transporter-atsweet10-to-modulate-stress-response-in-arabidopsis
#11
Ujjal J Phukan, Gajendra Singh Jeena, Vineeta Tripathi, Rakesh Kumar Shukla
As waterlogging and successive events severely influence growth and development of economically important plants, we attempted to characterize the role of a waterlogging-responsive Group I (A-6) Ethylene response factor (MaRAP2-4) from Mentha arvensis. Waterlogging, ethylene and Methyl jasmonate rapidly induced the expression of MaRAP2-4. MaRAP2-4 interacted with multiple cis-elements like Dehydration response elements (DRE1/2), Anoxia/Jasmonic acid response element (JARE) and GCC box showing its involvement in multiple responses...
June 21, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28625133/recent-advances-in-targeting-the-hiv-1-tat-tar-complex
#12
Fardokht A Abulwerdi, Stuart F J Le Grice
Following seminal discoveries by Rosen and co-workers in 1985, the HIV-1 TAR has emerged as one of the most extensively studied regulatory elements of the HIV-1 genome. Located adjacent to the long terminal repeat promoter, this cis-acting motif, in conjunction with the viral Tat protein, plays a critical role in viral genomic RNA synthesis via modification of the transcription complex. As such, the Tat/TAR axis has been the subject of intense efforts aimed at developing therapeutic interventions, directed against both the protein and nucleic acid components...
June 15, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28624228/antisense-oligonucleotides-promote-exon-inclusion-and-correct-the-common-c-32-13t-g-gaa-splicing-variant-in-pompe-disease
#13
Erik van der Wal, Atze J Bergsma, Joon M Pijnenburg, Ans T van der Ploeg, W W M Pim Pijnappel
The most common variant causing Pompe disease is c.-32-13T>G (IVS1) in the acid α-glucosidase (GAA) gene, which weakens the splice acceptor of GAA exon 2 and induces partial and complete exon 2 skipping. It also allows a low level of leaky wild-type splicing, leading to a childhood/adult phenotype. We hypothesized that cis-acting splicing motifs may exist that could be blocked using antisense oligonucleotides (AONs) to promote exon inclusion. To test this, a screen was performed in patient-derived primary fibroblasts using a tiling array of U7 small nuclear RNA (snRNA)-based AONs...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28613112/a-model-for-evolution-and-regulation-of-nicotine-biosynthesis-regulon-in-tobacco
#14
Masataka Kajikawa, Nicolas Sierro, Takashi Hashimoto, Tsubasa Shoji
In tobacco, the defense alkaloid nicotine is produced in roots and accumulates mainly in leaves. Signaling mediated by jasmonates (JAs) induces the formation of nicotine via a series of structural genes that constitute a regulon and are coordinated by JA-responsive transcription factors of the ethylene response factor (ERF) family. Early steps in the pyrrolidine and pyridine biosynthesis pathways likely arose through duplication of the polyamine and nicotinamide adenine dinucleotide (NAD) biosynthetic pathways, respectively, followed by recruitment of duplicated primary metabolic genes into the nicotine biosynthesis regulon...
June 14, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28607146/epigenetic-transcriptional-memory-of-gal-genes-depends-on-growth-in-glucose-and-the-tup1-transcription-factor-in-saccharomyces-cerevisiae
#15
Varun Sood, Ivelisse Cajigas, Agustina D'Urso, William H Light, Jason H Brickner
Previously expressed inducible genes can remain poised for faster reactivation for multiple cell divisions, a conserved phenomenon called epigenetic transcriptional memory. The GAL genes in Saccharomyces cerevisiae show faster reactivation for up to seven generations after being repressed. During memory, previously produced Gal1 protein enhances the rate of reactivation of GAL1, GAL10, GAL2 and GAL7 These genes also interact with the nuclear pore complex (NPC) and localize to the nuclear periphery both when active and during memory...
June 12, 2017: Genetics
https://www.readbyqxmd.com/read/28594957/distinctive-features-and-differential-regulation-of-the-drts-genes-of-arabidopsis-thaliana
#16
Antonio Maniga, Stefania Ghisaura, Lara Perrotta, Maria Giovanna Marche, Rino Cella, Diego Albani
In plants and protists, dihydrofolate reductase (DHFR) and thymidylate synthase (TS) are part of a bifunctional enzyme (DRTS) that allows efficient recycling of the dihydrofolate resulting from TS activity. Arabidopsis thaliana possesses three DRTS genes, called AtDRTS1, AtDRTS2 and AtDRTS3, that are located downstream of three members of the sec14-like SFH gene family. In this study, a characterization of the AtDRTS genes identified alternatively spliced transcripts coding for AtDRTS isoforms which may account for monofunctional DHFR enzymes supporting pathways unrelated to DNA synthesis...
2017: PloS One
https://www.readbyqxmd.com/read/28584068/genomic-insights-into-the-evolution-of-the-nicotine-biosynthesis-pathway-in-tobacco
#17
Masataka Kajikawa, Nicolas Sierro, Haruhiko Kawaguchi, Nicolas Bakaher, Nikolai V Ivanov, Takashi Hashimoto, Tsubasa Shoji
In tobacco (Nicotiana tabacum), nicotine is the predominant alkaloid. It is produced in the roots and accumulated mainly in the leaves. Jasmonates play a central signaling role in damage-induced nicotine formation. The genome sequence of tobacco provides us an almost complete inventory of structural and regulatory genes involved in nicotine pathway. Phylogenetic and expression analyses revealed a series of structural genes of the nicotine pathway, forming a regulon, under the control of jasmonate-responsive ETHYLENE RESPONSE FACTOR (ERF) transcription factors...
June 2017: Plant Physiology
https://www.readbyqxmd.com/read/28559488/viral-dna-replication-orientation-and-hnrnps-regulate-transcription-of-the-human-papillomavirus-18-late-promoter
#18
Xiaohong Wang, Haibin Liu, Hui Ge, Masahiko Ajiro, Nishi R Sharma, Craig Meyers, Pavel Morozov, Thomas Tuschl, Amar Klar, Donald Court, Zhi-Ming Zheng
The life cycle of human papillomaviruses (HPVs) is tightly linked to keratinocyte differentiation. Although expression of viral early genes is initiated immediately upon virus infection of undifferentiated basal cells, viral DNA amplification and late gene expression occur only in the mid to upper strata of the keratinocytes undergoing terminal differentiation. In this report, we show that the relative activity of HPV18 TATA-less late promoter P811 depends on its orientation relative to that of the origin (Ori) of viral DNA replication and is sensitive to the eukaryotic DNA polymerase inhibitor aphidicolin...
May 30, 2017: MBio
https://www.readbyqxmd.com/read/28549169/regulatory-dynamics-of-11p13-suggest-a-role-for-ehf-in-modifying-cf-lung-disease-severity
#19
Lindsay R Stolzenburg, Rui Yang, Jenny L Kerschner, Sara Fossum, Matthew Xu, Andrew Hoffmann, Kay-Marie Lamar, Sujana Ghosh, Sarah Wachtel, Shih-Hsing Leir, Ann Harris
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF), but are not good predictors of lung phenotype. Genome-wide association studies (GWAS) previously identified additional genomic sites associated with CF lung disease severity. One of these, at chromosome 11p13, is an intergenic region between Ets homologous factor (EHF) and Apaf-1 interacting protein (APIP). Our goal was to determine the functional significance of this region, which being intergenic is probably regulatory...
May 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28545024/an-unusual-intragenic-promoter-of-piwil2-contributes-to-aberrant-activation-of-oncogenic-pl2l60
#20
Shan-Shan Liu, Ning Liu, Meng-Yao Liu, Lei Sun, Wu-Yan Xia, Hong-Min Lu, Yu-Jie Fu, Guo-Liang Yang, Juan-Jie Bo, Xiao-Xing Liu, Haizhong Feng, Hailong Wu, Lin-Feng Li, Jian-Xin Gao
PIWIL2-like (PL2L) protein 60 (PL2L60), a product of aberrantly activated PIWIL2 gene, is widely expressed in various types of tumors and may promote tumorigenesis. However, the mechanisms underlying the activation of expression of PL2L60 remain unknown. In this study, an intragenic promoter responsible for the activation of PL2L60 within the human PIWIL2 gene has been identified, cloned and characterized. The promoter of PL2L60 is located in the intron 10 of the host gene PIWIL2. Bioinformatic and mutagenic analysis reveals that this intragenic promoter within the sequence of 50 nucleotides contains two closely arranged cis-acting elements specific for the hepatic leukemia factor (HLF) in the positive strand and signal transducer and activator of transcription 3 (STAT3) in the negative strand...
July 11, 2017: Oncotarget
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