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eukaryotic gene regulation

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https://www.readbyqxmd.com/read/28214582/structural-changes-induced-by-l50p-and-i61t-single-mutations-of-ubiquitin-affect-cell-cycle-progression-while-impairing-its-regulatory-and-degradative-functions-in-saccharomyces-cerevisiae
#1
Ankita Doshi, Mrinal Sharma, C Ratna Prabha
Posttranslational conjugation of ubiquitin to proteins either regulates their function directly or concentration through ubiquitination dependent degradation. High degree of conservation of ubiquitin's sequence implies structural and functional importance of the conserved residues. Ubiquitin gene of Saccharomyces cerevisiae was evolved in vitro by us to study the significance of conserved residues. Present study investigates the structural changes in the protein resulting from the single mutations UbS20F, UbA46S, UbL50P, UbI61T and their functional consequences in the SUB60 strain of S...
February 15, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28213158/pink1-parkin-mitophagy-and-neurodegeneration-what-do-we-really-know-in-vivo
#2
REVIEW
Alexander J Whitworth, Leo J Pallanck
Mitochondria are essential organelles that provide cellular energy and buffer cytoplasmic calcium. At the same time they produce damaging reactive oxygen species and sequester pro-apoptotic factors. Hence, eukaryotes have evolved exquisite homeostatic processes that maintain mitochondrial integrity, or ultimately remove damaged organelles. This subject has garnered intense interest recently following the discovery that two Parkinson's disease genes, PINK1 and parkin, regulate mitochondrial degradation (mitophagy)...
February 14, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28209632/high-resolution-profiling-of-nmd-targets-in-yeast-reveals-translational-fidelity-as-a-basis-for-substrate-selection
#3
Alper Celik, Richard Baker, Feng He, Allan Jacobson
Nonsense-mediated mRNA decay (NMD) plays an important role in eukaryotic gene expression yet the scope and the defining features of NMD-targeted transcripts remain elusive. To address these issues, we re-evaluated the genome-wide expression of annotated transcripts in yeast cells harboring deletions of the UPF1, UPF2, or UPF3 genes. Our new RNA-Seq analyses confirm previous results of microarray studies, but also uncover hundreds of new NMD-regulated transcripts that had escaped previous detection, including many intron-containing pre-mRNAs and several non-coding RNAs...
February 16, 2017: RNA
https://www.readbyqxmd.com/read/28207814/jmjd-5-kdm8-regulates-h3k36me2-and-is-required-for-late-steps-of-homologous-recombination-and-genome-integrity
#4
Pier Giorgio Amendola, Nico Zaghet, João J Ramalho, Jens Vilstrup Johansen, Mike Boxem, Anna Elisabetta Salcini
The eukaryotic genome is organized in a three-dimensional structure called chromatin, constituted by DNA and associated proteins, the majority of which are histones. Post-translational modifications of histone proteins greatly influence chromatin structure and regulate many DNA-based biological processes. Methylation of lysine 36 of histone 3 (H3K36) is a post-translational modification functionally relevant during early steps of DNA damage repair. Here, we show that the JMJD-5 regulates H3K36 di-methylation and it is required at late stages of double strand break repair mediated by homologous recombination...
February 16, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28205535/phylogenetic-analysis-of-eukaryotic-neet-proteins-uncovers-a-link-between-a-key-gene-duplication-event-and-the-evolution-of-vertebrates
#5
Madhuri A Inupakutika, Soham Sengupta, Rachel Nechushtai, Patricia A Jennings, Jose' N Onuchic, Rajeev K Azad, Pamela Padilla, Ron Mittler
NEET proteins belong to a unique family of iron-sulfur proteins in which the 2Fe-2S cluster is coordinated by a CDGSH domain that is followed by the "NEET" motif. They are involved in the regulation of iron and reactive oxygen metabolism, and have been associated with the progression of diabetes, cancer, aging and neurodegenerative diseases. Despite their important biological functions, the evolution and diversification of eukaryotic NEET proteins are largely unknown. Here we used the three members of the human NEET protein family (CISD1, mitoNEET; CISD2, NAF-1 or Miner 1; and CISD3, Miner2) as our guides to conduct a phylogenetic analysis of eukaryotic NEET proteins and their evolution...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28203225/regulation-of-sterol-biosynthesis-in-the-human-fungal-pathogen-aspergillus-fumigatus-opportunities-for-therapeutic-development
#6
REVIEW
Sourabh Dhingra, Robert A Cramer
Sterols are a major component of eukaryotic cell membranes. For human fungal infections caused by the filamentous fungus Aspergillus fumigatus, antifungal drugs that target sterol biosynthesis and/or function remain the standard of care. Yet, an understanding of A. fumigatus sterol biosynthesis regulatory mechanisms remains an under developed therapeutic target. The critical role of sterol biosynthesis regulation and its interactions with clinically relevant azole drugs is highlighted by the basic helix loop helix (bHLH) class of transcription factors known as Sterol Regulatory Element Binding Proteins (SREBPs)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28202675/the-molecular-basis-of-mtorc1-regulated-translation
#7
REVIEW
Carson C Thoreen
The mammalian target of rapamycin (mTOR) signaling pathway is a master regulator of cell growth throughout eukaryotes. The pathway senses nutrient and other growth signals, and then orchestrates the complex systems of anabolic and catabolic metabolism that underpin the growth process. A central target of mTOR signaling is the translation machinery. mTOR uses a multitude of translation factors to drive the bulk production of protein that growth requires, but also to direct a post-transcriptional program of growth-specific gene expression...
February 8, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28202544/cdc15-phosphorylates-carboxy-terminal-domain-of-rna-polymerase-ii-for-transcription-during-mitosis
#8
Amit Kumar Singh, Shivangi Rastogi, Harish Shukla, Mohd Asalam, Srikanta Kumar Rath, Md Sohail Akhtar
In eukaryotes, the basal transcription in interphase is orchestrated through the regulation by kinases (Kin28, Bur1 and Ctk1) and phosphatases (Ssu72, Rtr1 and Fcp1) which act through the post-translational modification of CTD (carboxy terminal domain of the largest subunit of RNA Polymerase II). The CTD comprises of repeated Tyr1Ser2Pro3Thr4Ser5Pro6Ser7 motif with potential epigenetic modification sites. Despite the observation of transcription and periodic expression of genes during mitosis with entailing CTD phosphorylation and dephosphorylation, the associated CTD specific kinase/s and its role in transcription remains unknown...
February 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28199212/transposon-mediated-directed-mutation-in-bacteria-and-eukaryotes
#9
Milton H Saier, Chika Kukita, Zhongge Zhang
Transposon-mediated "directed" mutations occur at higher frequencies when beneficial than when detrimental and relieve the stress that causes them. The first and best-studied example involves regulation of Insertion Sequence-5 (IS5) insertion into a specific activating site upstream of the glycerol utilization operon in Escherichia coli, glpFK. This event promotes high level expression of the glpFK operon, allowing glycerol utilization in wild type cells under inhibitory conditions. The phosphoenolpyruvate-dependent, sugar transporting, phosphotransferase system (PTS) influences this process by regulating cytoplasmic glycerol-3-phosphate and cyclic AMP concentrations...
March 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28194319/candidate-genes-that-have-facilitated-freshwater-adaptation-by-palaemonid-prawns-in-the-genus-macrobrachium-identification-and-expression-validation-in-a-model-species-m-koombooloomba
#10
Md Lifat Rahi, Shorash Amin, Peter B Mather, David A Hurwood
BACKGROUND: The endemic Australian freshwater prawn, Macrobrachium koombooloomba, provides a model for exploring genes involved with freshwater adaptation because it is one of the relatively few Macrobrachium species that can complete its entire life cycle in freshwater. METHODS: The present study was conducted to identify potential candidate genes that are likely to contribute to effective freshwater adaptation by M. koombooloomba using a transcriptomics approach...
2017: PeerJ
https://www.readbyqxmd.com/read/28193673/structure-of-the-escherichia-coli-proq-rna-chaperone-protein
#11
Grecia Gonzalez, Steven Hardwick, Sarah L Maslen, J Mark Skehel, Erik Holmqvist, Jörg Vogel, Alex Bateman, Ben Luisi, R William Broadhurst
The protein ProQ has recently been identified as a global RNA chaperone in Salmonella, and a similar role is anticipated for its numerous homologues in divergent bacterial species. We report the solution structure of Escherichia coli ProQ, revealing an N-terminal FinO-like domain, a C-terminal domain that unexpectedly has a Tudor-domain fold commonly found in eukaryotes, and an elongated bridging intra-domain linker that is flexible but nonetheless incompressible. Structure based sequence analysis suggests that the Tudor domain was acquired through horizontal gene transfer and gene fusion to the ancestral FinO-like domain...
February 13, 2017: RNA
https://www.readbyqxmd.com/read/28192619/genomic-signatures-of-adaptation-to-wine-biological-aging-conditions%C3%A2-in-biofilm-forming-flor-yeasts
#12
A L Coi, F Bigey, S Mallet, S Marsit, G Zara, P Gladieux, V Galeote, M Budroni, S Dequin, J L Legras
The molecular and evolutionary processes underlying fungal domestication remain largely unknown despite the importance of fungi to bioindustry and for comparative adaptation genomics in eukaryotes. Wine fermentation and biological aging are performed by strains of S. cerevisiae with, respectively, pelagic fermentative growth on glucose, and biofilm aerobic growth utilizing ethanol. Here, we use environmental samples of wine and flor yeasts to investigate the genomic basis of yeast adaptation to contrasted anthropogenic environments...
February 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28188284/glucagon-and-insulin-cooperatively-stimulate-fibroblast-growth-factor-21-gene-transcription-by-increasing-the-expression-of-activating-transcription-factor-4
#13
Kimberly M Alonge, Gordon P Meares, F Bradley Hillgartner
Previous studies have shown that glucagon cooperatively interacts with insulin to stimulate hepatic fibroblast growth factor 21 (FGF21) gene expression. Here, we investigated the mechanism by which glucagon and insulin increased FGF21 gene transcription in primary hepatocyte cultures. Transfection analyses demonstrated that glucagon plus insulin induction of FGF21 transcription was conferred by two activating transcription factor 4 (ATF4) binding sites in the FGF21 gene. Glucagon plus insulin stimulated a 5-fold increase in ATF4 protein abundance, and knockdown of ATF4 expression suppressed the ability of glucagon plus insulin to increase FGF21 expression...
February 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28185554/evolution-of-transcriptional-networks-in-yeast-alternative-teams-of-transcriptional-factors-for-different-species
#14
Adriana Muñoz, Daniella Santos Muñoz, Aleksey Zimin, James A Yorke
BACKGROUND: The diversity in eukaryotic life reflects a diversity in regulatory pathways. Nocedal and Johnson argue that the rewiring of gene regulatory networks is a major force for the diversity of life, that changes in regulation can create new species. RESULTS: We have created a method (based on our new "ping-pong algorithm) for detecting more complicated rewirings, where several transcription factors can substitute for one or more transcription factors in the regulation of a family of co-regulated genes...
November 11, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28182317/impact-of-light-intensity-and-quality-on-chromatophore-and-nuclear-gene-expression-in-paulinella-chromatophora-an-amoeba-with-nascent-photosynthetic-organelles
#15
Ru Zhang, Eva C M Nowack, Dana C Price, Debashish Bhattacharya, Arthur R Grossman
Plastid evolution has been attributed to a single primary endosymbiotic event that occurred ~1.6 BYA in which a cyanobacterium was engulfed and retained by a eukaryotic cell, although early steps in plastid integration are poorly understood. The photosynthetic amoeba Paulinella chromatophora represents a unique model to study plastid evolution because it contains cyanobacterium-derived photosynthetic organelles termed "chromatophores" that originated relatively recently (0.06-0.14 BYA). The chromatophore genome is ~1/3 the size of the genome of closely related cyanobacteria, but 10-fold larger than most plastid genomes...
February 9, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28179524/two-white-spot-syndrome-virus-mirnas-target-dorsal-to-promote-virus-infection-in-shrimp-marsupenaeus-japonicas
#16
Qian Ren, Xin Huang, Yalei Cui, Jiejie Sun, Wen Wang, Xiaobo Zhang
In eukaryotes, microRNAs (miRNAs) serve as regulators of many biological processes, including virus infection. A miRNA can generally target diverse genes during virus-host interactions. However, regulation of gene expression by multiple miRNAs has not yet been extensively explored during virus infection. This study found that the Spz-Toll-Dorsal-ALF signaling pathway played a very important role in antiviral immunity in shrimp (Marsupenaeus japonicus) against invasion of white spot syndrome virus (WSSV). Dorsal, the central gene in Toll pathway, was targeted by two viral miRNAs (WSSV-miR-N13 and WSSV-miR-N23) during WSSV infection...
February 8, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28179399/differential-proteomics-profiling-identifies-lipid-droplet-proteins-and-biological-functions-in-high-fat-diet-induced-fatty-livers
#17
Mingwei Liu, Rui Ge, Wanlin Liu, Qiongming Liu, Xia Xia, Mi Lai, Lizhu Liang, Chen Li, Lei Song, Bei Zhen, Jun Qin, Chen Ding
Eukaryotic cells store neutral lipids in cytoplasmic lipid droplets (LD) enclosed in a monolayer of phospholipids and associated proteins (LDP). Growing evidence has demonstrated that LDPs play important roles in the pathogenesis of liver diseases. However, the composition of liver LDPs and role of their alterations in hepatosteatosis is not well understood. In this study, we performed liver proteome and lipid droplet sub-proteome profiling to identify enriched proteins in LD as LDPs, and quantified their changes in a high fat diet induced (HFD) fatty liver model...
February 8, 2017: Journal of Lipid Research
https://www.readbyqxmd.com/read/28177216/bacterioferritin-structure-dynamics-and-protein-protein-interactions-at-play-in-iron-storage-and-mobilization
#18
Mario Rivera
Despite its essentiality to life, iron presents significant challenges to cells: the exceedingly low solubility of Fe(3+) limits its bioavailability, and the reactivity of Fe(2+) toward H2O2 is a source of the toxic hydroxyl radical (HO(•)). Consequently, cellular levels of free iron are highly regulated to ensure sufficiency while preventing iron-induced toxicity. Relatively little is known about the fate of iron in the bacterial cytosol or how cells balance the need for relatively high cytosolic iron concentrations with the potential toxicity of the nutrient...
February 8, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28167521/ddar-pa1196-regulates-expression-of-dimethylarginine-dimethylaminohydrolase-for-the-metabolism-of-methylarginines-in-pseudomonas-aeruginosa-pao1
#19
Benjamin R Lundgren, Frank J Bailey, Gabriella Moley, Christopher T Nomura
: Dimethylarginine dimethylaminohydrolases or DDAHs catalyze the hydrolysis of methylarginines to yield L-citrulline and methylamines as products. DDAHs and their central roles in methylarginine metabolism have been characterized for eukaryotic cells. While DDAHs are known to exist in some bacteria, including Streptomyces coelicolor and Pseudomonas aeruginosa, the physiological importance and genetic regulation of bacterial DDAHs remain poorly understood. To provide some insight into bacterial methylarginine metabolism, this study focused on identifying the key elements or factors regulating DDAH expression in P...
February 6, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28167048/biochemical-fractionation-of-time-resolved-drosophila-embryos-reveals-similar-transcriptomic-alterations-in-replication-checkpoint-and-histone-mrna-processing-mutants
#20
Fabio Alexis Lefebvre, Louis Philip Benoit Bouvrette, Julie Bergalet, Eric Lécuyer
In higher eukaryotes, maternally provided gene products drive the initial stages of embryogenesis until the zygotic transcriptional program takes over, a developmental process called the midblastula transition (MBT). In addition to zygotic genome activation, the MBT involves alterations in cell-cycle length and the implementation of DNA damage/replication checkpoints that serve to monitor genome integrity. Previous work has shown that mutations affecting histone mRNA metabolism or DNA replication checkpoint factors severely impact developmental progression through the MBT, prompting us to characterize and contrast the transcriptomic impact of these genetic perturbations...
February 3, 2017: Journal of Molecular Biology
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