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Daniel M Cohen, Hee-Woong Lim, Kyoung-Jae Won, David J Steger
Sequence-specific DNA binding recruits transcription factors (TFs) to the genome to regulate gene expression. Here, we perform high resolution mapping of CEBP proteins to determine how sequence dictates genomic occupancy. We demonstrate a fundamental difference between the sequence repertoire utilized by CEBPs in vivo versus the palindromic sequence preference reported by classical in vitro models, by identifying a palindromic motif at <1% of the genomic binding sites. On the native genome, CEBPs bind a diversity of related 10 bp sequences resulting from the fusion of degenerate and canonical half-sites...
July 31, 2018: Nucleic Acids Research
Jianbo Yuan, Yuqing Bai, Yuehui Chao, Xinbo Sun, Chunyan He, Xiaohong Liang, Lijuan Xie, Liebao Han
Cadmium (Cd) toxicity seriously affects the growth and development of plants, so studies on uptake, translocation, and accumulation of Cd in plants are crucial for phytoremediation. However, the molecular mechanism of the plant response to Cd stress remains poorly understood. The main objective of this study was to reveal differentially expressed genes (DEGs) under lower (BT2_5) and higher (BT43) Cd concentration treatments in creeping bentgrass. A total of 463,184 unigenes were obtained from creeping bentgrass leaves using RNA sequencing technology...
2018: PeerJ
Chang-Hyun Lee, Marianthi Kiparaki, Jorge Blanco, Virginia Folgado, Zhejun Ji, Amit Kumar, Gerard Rimesso, Nicholas E Baker
Ribosomes perform protein synthesis but are also involved in signaling processes, the full extent of which are still being uncovered. We report that phenotypes of mutating ribosomal proteins (Rps) are largely due to signaling. Using Drosophila, we discovered that a bZip-domain protein, Xrp1, becomes elevated in Rp mutant cells. Xrp1 reduces translation and growth, delays development, is responsible for gene expression changes, and causes the cell competition of Rp heterozygous cells from genetic mosaics. Without Xrp1, even cells homozygously deleted for Rp genes persist and grow...
August 1, 2018: Developmental Cell
Da-Hye Kim, Sangkyu Park, Jong-Yeol Lee, Sun-Hwa Ha, Jun-Gu Lee, Sun-Hyung Lim
Anthocyanins are responsible pigments for giving attractive colors of plant organs and nutraceutical benefits of grains. Anthocyanin biosynthesis is known to be regulated by transcription factors and other regulatory proteins. In rice ( Oryza sativa ), the R2R3 MYB transcription factor (TF) OsC1 and a bHLH TF, OsB2, were previously reported to control anthocyanin biosynthesis in vegetative tissues and seeds, respectively; however, the regulatory mechanisms of the anthocyanin biosynthesis by TFs remain largely unknown...
July 27, 2018: International Journal of Molecular Sciences
Yan Wang, Liuqing Wang, Fan Wu, Fei Liu, Qi Wang, Xiaoling Zhang, Jonathan Nimal Selvaraj, Yueju Zhao, Fuguo Xing, Wen-Bing Yin, Yang Liu
Ochratoxin A (OTA) is a toxic secondary metabolite produced by Aspergillus and Penicillium species that widely contaminate food and feed. We sequenced and assembled the complete ∼37 Mb genome of A. ochraceus fc-1, a well-known producer of OTA. Key genes of the OTA biosynthetic pathway were identified by comparative genomic analyses with five other sequenced OTA-producing fungi, A. carbonarius , A. niger , A. steynii , A. westerdijkiae , and Penicillium nordicum OTA production was completely inhibited in the deletion mutants ( ΔotaA - D and ΔotaR1 ), and OTA biosynthesis was restored by feeding a post-block substrate to the corresponding mutant...
July 27, 2018: Applied and Environmental Microbiology
Yin Li, Wenqin Wang, Yaping Feng, Min Tu, Peter E Wittich, Nicholas J Bate, Joachim Messing
Sweet sorghum accumulates large amounts of soluble sugar in its stem. However, a system-based understanding of this carbohydrate allocation process is lacking. Here, we compared the dynamic transcriptome and metabolome between the conversion line R9188 and its two parents, sweet sorghum RIO and grain sorghum BTx406 that have contrasting sugar-accumulating phenotypes. We identified two features of sucrose metabolism, stable concentrations of sugar phosphates in RIO and opposite trend of trehalose-6-phosphate (T6P) between RIO versus R9188/BTx406...
July 26, 2018: Plant Biotechnology Journal
Chae Woo Lim, Woonhee Baek, Sung Chul Lee
Abscisic acid (ABA) is a plant hormone that plays a key role in the environmental stress response, especially induction of ABA- and stress-responsive genes and modulation of the stomatal aperture in response to drought stress. Here, we identified CaDILZ1 (Capsicum annuum Drought-Induced Leucine Zipper 1) belonging to subgroup D of the bZIP protein family; gene functions of this family in response to ABA and drought signaling still remain unknown. CaDILZ1 expression was significantly induced in pepper leaves after exposure to ABA, drought, and NaCl...
July 27, 2018: Plant Journal: for Cell and Molecular Biology
Lu Qiu, Meng Wang, Yuping Zhu, Yuancai Xiang, Yiguo Zhang
Transcription factor Nrf2 (nuclear factor-erythroid 2-related factor 2) is a master regulator of antioxidant and/or electrophile response elements (AREs/EpREs)-driven genes involved in homeostasis, detoxification, and adaptation to various stresses. The cytoprotective activity of Nrf2, though being oppositely involved in both cancer prevention and progression, is critically controlled by Keap1 (Kelch-like ECH-associated protein 1), which is an adaptor subunit of Cullin 3-based E3 ubiquitin ligase and also is a key sensor for oxidative and electrophilic stresses...
July 24, 2018: International Journal of Molecular Sciences
Farina A Beinecke, Lena Grundmann, David R Wiedmann, Florentin J Schmidt, Andrea S Caesar, Marius Zimmermann, Michael Lahme, Richard M Twyman, Dirk Prüfer, Gundula A Noll
Photoperiod is an important external stimulus governing the precise timing of the floral transition in plants. Members of the FLOWERING LOCUS T (FT)-like clade of phosphatidylethanolamine-binding proteins induce this developmental process in numerous species by forming regulatory protein complexes with FD-like bZIP transcription factors. We identified several thus far unknown FT-like and FD-like genes in the genus Nicotiana and found that, even in the day-neutral species N. tabacum, floral initiation requires the photoperiod-dependent expression of several FT-like genes...
July 21, 2018: Plant Journal: for Cell and Molecular Biology
Xiaoji Wang, Can Guo, Jing Peng, Cong Li, Fangfang Wan, Shaoman Zhang, Yangyang Zhou, Yan Yan, Lijuan Qi, Kaiwen Sun, Shuhua Yang, Zhizhong Gong, Jigang Li
Group A protein phosphatase 2Cs (PP2Cs) are abscisic acid (ABA) co-receptors that negatively regulate the ABA signaling pathway by inhibiting the downstream SnRK2 protein kinases. It has long been observed that exogenous ABA treatments dramatically induce the expression of group A PP2C genes, but the underlying molecular mechanisms and the biological significance remain largely unknown. Here, by using GUS reporter transgenic lines in which various lengths of ABI1 and ABI2 promoters were used to drive GUS gene expression, we defined the promoter fragments that confer ABA inducibility to ABI1 and ABI2...
July 18, 2018: New Phytologist
Yanyan Wang, Yujuan Zhang, Rong Zhou, Komivi Dossa, Jingyin Yu, Donghua Li, Aili Liu, Marie Ali Mmadi, Xiurong Zhang, Jun You
Basic leucine zipper (bZIP) gene family is one of the largest transcription factor families in plants, and members of this family play important roles in multiple biological processes such as light signaling, seed maturation, flower development as well as abiotic and biotic stress responses. Nonetheless, genome-wide comprehensive analysis of the bZIP family is lacking in the important oil crop sesame. In the present study, 63 bZIP genes distributed on 14 linkage groups were identified in sesame, and denominated as SibZIP01-SibZIP63...
2018: PloS One
Daisuke Tsugama, Shenkui Liu, Kaien Fujino, Tetsuo Takano
Background and Aims: VIP1 is a bZIP transcription factor in Arabidopsis thaliana. VIP1 and its close homologues transiently accumulate in the nucleus when cells are exposed to hypo-osmotic and/or mechanical stress. Touch-induced root bending is enhanced in transgenic plants overexpressing a repression domain-fused form of VIP1 (VIP1-SRDXox), suggesting that VIP1, possibly with its close homologues, suppresses touch-induced root bending. The aim of this study was to identify regulators of these functions of VIP1 in mechanical stress responses...
July 14, 2018: Annals of Botany
Milad Iranshahy, Mehrdad Iranshahi, Seyed Reza Abtahi, Gholamreza Karimi
Internal metabolism and environmental toxicant exposure can be caused to generate reactive oxygen species in human organelles which lead to oxidative stress. The nuclear factor erythroid 2-related factor 2 (Nrf2), a basic leucine zipper (bZip) transcription factor, controls the expression of antioxidant response element (ARE)-dependent genes to regulate cellular resistance to oxidants. Nrf2 is an essential factor for hepatoprotection against drugs and xenobiotics. The key role of Nrf2 in hepatoprotection has been highlighted since Nrf2 knockout mice showed high sensitivity to xenobiotic-induced hepatotoxicity...
July 14, 2018: Food and Chemical Toxicology
Johanna K Freundt, Gerrit Frommeyer, Fabian Wötzel, Andreas Huge, Andreas Hoffmeier, Sven Martens, Lars Eckardt, Philipp S Lange
Introduction: Cardiomyocyte remodelling in atrial fibrillation (AF) has been associated with both oxidative stress and endoplasmic reticulum (ER) stress and is accompanied by a complex transcriptional regulation. Here, we investigated the role the oxidative stress and ER stress responsive bZIP transcription factor ATF4 plays in atrial cardiomyocyte viability and AF induced gene expression. Methods: HL-1 cardiomyocytes were subjected to rapid field stimulation. Forced expression of ATF4 was achieved by adenoviral gene transfer...
2018: BioMed Research International
Mohammad Amin Omidbakhshfard, Ushio Fujikura, Justyna Jadwiga Olas, Gang-Ping Xue, Salma Balazadeh, Bernd Mueller-Roeber
Leaf growth is a complex process that involves the action of diverse transcription factors (TFs) and their downstream gene regulatory networks. In this study, we focus on the functional characterization of the Arabidopsis thaliana TF GROWTH-REGULATING FACTOR9 (GRF9) and demonstrate that it exerts its negative effect on leaf growth by activating expression of the bZIP TF OBP3-RESPONSIVE GENE 3 (ORG3). While grf9 knockout mutants produce bigger incipient leaf primordia at the shoot apex, rosette leaves and petals than the wild type, the sizes of those organs are reduced in plants overexpressing GRF9 (GRF9ox)...
July 2018: PLoS Genetics
Yipeng Ren, Jiaqing Zhang, Wenhao Dong, Huanhuan Yang, Baoping Pan, Wenjun Bu
The transcription factor activator protein-1 (AP-1) plays an essential and critical role in the regulation of numerous downstream genes involved in various physiological and chemical responses. In this study, we identified a full-length cDNA of the c-Jun AP-1 gene (termed Csc-Jun) from the transcriptome library in Cyclina sinensis. The cDNA contains an 825-bp open reading frame that encodes a 274-amino acid protein sequence, including a characteristic Jun transcription factor domain and a highly conserved basic leucine zipper (bZIP) signature that shares 90% identity to that of Ruditapes philippinarum...
July 3, 2018: Developmental and Comparative Immunology
Ji-Min Lee, Hye-Sook Han, Yoon Seok Jung, Robert A Harris, Seung-Hoi Koo, Hueng-Sik Choi
Under fasting conditions, activation of several hepatic genes sets the stage for gluconeogenesis in the liver. cAMP response element-binding protein (CREB), CREB-regulated transcription coactivator 2 (CRTC2), and peroxisome proliferator-activated receptor γ coactivator 1-alpha (PGC-1α) are essential for this transcriptional induction of gluconeogenic genes. PGC-1α induction is mediated by activation of a CREB/CRCT2 signaling complex, and recent findings have revealed that small heterodimer partner-interacting leucine zipper protein (SMILE), a member of the CREB/ATF family of basic region-leucine zipper (bZIP) transcription factors, is an insulin-inducible corepressor that decreases PGC-1α expression and abrogates its stimulatory effect on hepatic gluconeogenesis...
June 27, 2018: Journal of Biological Chemistry
Bizunesh Abere, Naira Samarina, Silvia Gramolelli, Jessica Rückert, Gisa Gerold, Andreas Pich, Thomas F Schulz
Kaposi's sarcoma-associated herpesvirus (KSHV)/Human herpesvirus-8 (HHV-8) causes the angiogenic tumor Kaposi's Sarcoma (KS) and two B-cell malignancies. The KSHV non-structural membrane protein encoded by open reading frame (orf) K15 recruits and activates several cellular proteins including PLCγ1, components of the NF-κB pathway as well as members of the Src family of non-receptor tyrosine kinases and thereby plays an important role in the activation of angiogenic and inflammatory pathways that contribute to the pathogenesis of KS as well as KSHV productive (lytic) replication...
June 27, 2018: Journal of Virology
Citao Liu, Bigang Mao, Shujun Ou, Wei Wang, Linchuan Liu, Yanbin Wu, Chengcai Chu, Xiping Wang
Due to an error in combining the figure, an incorrect version of Fig. 9e was presented in the original publication.
July 2018: Plant Molecular Biology
Rachelle Lapham, Lan-Ying Lee, Daisuke Tsugama, Sanghun Lee, Tesfaye Mengiste, Stanton B Gelvin
The bZIP transcription factor VIP1 interacts with the Agrobacterium virulence protein VirE2, but the role of VIP1 in Agrobacterium -mediated transformation remains controversial. Previously tested vip1-1 mutant plants produce a truncated protein containing the crucial bZIP DNA-binding domain. We generated the CRISPR/Cas mutant vip1-2 that lacks this domain. The transformation susceptibility of vip1-2 and wild-type plants is similar. Because of potential functional redundancy among VIP1 homologs, we tested transgenic lines expressing VIP1 fused to a SRDX repression domain...
2018: Frontiers in Plant Science
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