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gene regulation in eukaryotes

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https://www.readbyqxmd.com/read/29340068/chaperonin-containing-tcp-1-subunit-3-is-critical-for-gastric-cancer-growth
#1
Li-Juan Li, Lian-Sheng Zhang, Zhi-Jian Han, Zhi-Yun He, Hao Chen, Yu-Min Li
Background: Members of eukaryotic chaperonin family are essential for cell survival. Dysregulation of Chaperonin containing TCP-1 subunit 3 (CCT3) has been implicated in the development of several types of cancers. However, the role of CCT3 in the development of gastric cancer has yet to be determined. Methods: The expression patterns of CCT3 in the surgical specimens from 26 gastric cancer patients were evaluated using immunohistochemistry methods. To study the possible roles of CCT3 in the growth and survival of gastric cancer cells, RNA interference was used to knockdown CCT3 expression in gastric cancer cell lines BGC-823 and MGC-803...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29339748/dot1-regulates-nucleosome-dynamics-by-its-inherent-histone-chaperone-activity-in-yeast
#2
Soyun Lee, Seunghee Oh, Kwiwan Jeong, Hyelim Jo, Yoonjung Choi, Hogyu David Seo, Minhoo Kim, Joonho Choe, Chang Seob Kwon, Daeyoup Lee
Dot1 (disruptor of telomeric silencing-1, DOT1L in humans) is the only known enzyme responsible for histone H3 lysine 79 methylation (H3K79me) and is evolutionarily conserved in most eukaryotes. Yeast Dot1p lacks a SET domain and does not methylate free histones and thus may have different actions with respect to other histone methyltransferases. Here we show that Dot1p displays histone chaperone activity and regulates nucleosome dynamics via histone exchange in yeast. We show that a methylation-independent function of Dot1p is required for the cryptic transcription within transcribed regions seen following disruption of the Set2-Rpd3S pathway...
January 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29338542/the-novel-microtubule-associated-cap-glycine-protein-cgp1-governs-growth-differentiation-and-virulence-of-cryptococcus-neoformans
#3
Li Li Wang, Kyung-Tae Lee, Kwang-Woo Jung, Dong-Gi Lee, Yong-Sun Bahn
Microtubules are involved in mechanical support, cytoplasmic organization, and several cellular processes by interacting with diverse microtubule-associated proteins such as plus-end tracking proteins, motor proteins, and tubulin-folding cofactors. A number of the cytoskeleton-associated proteins (CAPs) contain the CAP-glycine-rich (CAP-Gly) domain, which is evolutionarily conserved and generally considered to bind to α-tubulin to regulate the function of microtubules. However, there has been a dearth of research on CAP-Gly proteins in fungal pathogens, including Cryptococcus neoformans, which is a global cause of fatal meningoencephalitis in immunocompromised patients...
January 17, 2018: Virulence
https://www.readbyqxmd.com/read/29331583/importins-%C3%AE-and-%C3%AE-signaling-mediates-endothelial-cell-inflammation-and-barrier-disruption
#4
Antony Leonard, Arshad Rahman, Fabeha Fazal
Nucleocytoplasmic shuttling via importins is central to the function of eukaryotic cells and an integral part of the processes that lead to many human diseases. In this study, we addressed the role of α and β importins in the mechanism of endothelial cell (EC) inflammation and permeability, important pathogenic features of many inflammatory diseases such as acute lung injury and atherosclerosis. RNAi-mediated knockdown of importin α4 or α3 each inhibited NF-κB activation, proinflammatory gene (ICAM-1, VCAM-1, and IL-6) expression, and thereby endothelial adhesivity towards HL-60 cells, upon thrombin challenge...
January 10, 2018: Cellular Signalling
https://www.readbyqxmd.com/read/29331019/cis-regulator-runaway-and-divergence-in-asexuals
#5
Frédéric Fyon, Thomas Lenormand
With the advent of new sequencing technologies, the evolution of gene expression is becoming a subject of intensive genomic research, with sparking debates upon the role played by these kinds of changes in adaptive evolution and speciation. In this paper, we model expression evolution in species differing by their reproductive systems. We consider different rates of sexual versus asexual reproduction and the different type of parthenogenesis (apomixis and the various modes of automixis). We show that competition for expression leads to two selective processes on cis-regulatory regions that act independently to organism-level adaptation...
January 13, 2018: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29330104/circular-rna-an-emerging-non-coding-rna-as-a-regulator-and-biomarker-in-cancer
#6
Bing Chen, Shenglin Huang
Circular RNA (circRNA) is a type of covalently closed non-coding RNA that may regulate gene expression in eukaryotes. The recent application of high-throughput RNA sequencing and bioinformatics approaches has revealed a large number of circRNAs in human cells. Emerging evidence indicates that many circRNAs have cell-type specific expression and are linked to physiological development and various diseases. Specially, circRNAs can either serve as oncogenic stimuli or tumor suppressors in cancer. circRNAs have also been shown to be enriched and stable in extracellular fluid, indicating the potential of circRNAs as cancer biomarkers...
January 9, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29329439/conserved-proteins-of-the-rna-interference-system-in-the-arbuscular-mycorrhizal-fungus-rhizoglomus-irregulare-provide-new-insight-into-the-evolutionary-history-of-glomeromycota
#7
Soon-Jae Lee, Mengxuan Kong, Paul Harrison, Mohamed Hijri
Horizontal gene transfer (HGT) is an important mechanism in the evolution of many living organisms particularly in Prokaryotes where genes are frequently dispersed between taxa. Although, HGT has been reported in Eukaryotes, its accumulative effect and its frequency has been questioned. Arbuscular mycorrhizal fungi (AMF) are an early diverged fungal lineage belonging to phylum Glomeromycota, whose phylogenetic position is still under debate. The history of AMF and land plant symbiosis dates back to at least 460 million years ago...
January 10, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29324855/ctls-a-new-class-of-ring-h2-ubiquitin-ligases-uncovered-by-yeell-a-motif-close-to-the-ring-domain-that-is-present-across-eukaryotes
#8
Domingo Jiménez-López, Laura Aguilar-Henonin, Juan Manuel González-Prieto, Victor Aguilar-Hernández, Plinio Guzmán
RING ubiquitin E3 ligases enclose a RING domain for ubiquitin ligase activity and associated domains and/or conserved motifs outside the RING domain that collectively facilitate their classification and usually reveal some of key information related to mechanism of action. Here we describe a new family of E3 ligases that encodes a RING-H2 domain related in sequence to the ATL and BTL RING-H2 domains. This family, named CTL, encodes a motif designed as YEELL that expands 21 amino acids next to the RING-H2 domain that is present across most eukaryotic lineages...
2018: PloS One
https://www.readbyqxmd.com/read/29323924/akt-serine-threonine-kinase-1-regulates-de-novo-fatty-acid-synthesis-through-mtor-srebp1-axis-in-dairy-goat-mammary-epithelial-cells
#9
Tianying Zhang, Jiangtao Huang, Yongqing Yi, Xueying Zhang, Juan J Loor, Yanhong Cao, Huaiping Shi, Jun Luo
Akt serine/threonine kinase acts as a central mediator in the PI3K/Akt signaling pathway, regulating a series of biological processes. In lipid metabolism, Akt activation regulates a series of gene expressions, including genes related to intracellular fatty acid synthesis. However, the regulatory mechanisms of Akt in dairy goat mammary lipid metabolism have not been elaborated. In this study, the coding sequences of goat Akt1 gene were cloned and analyzed. Gene expression of Akt1 in different lactation stages was also investigated...
January 11, 2018: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29323132/assembly-of-an-atypical-%C3%AE-macroglobulin-complex-from-pseudomonas-aeruginosa
#10
Samira Zouhir, Mylène Robert-Genthon, Daniel Maragno Trindade, Viviana Job, Marko Nedeljković, Cécile Breyton, Christine Ebel, Ina Attrée, Andréa Dessen
Alpha-2-macroglobulins (A2Ms) are large spectrum protease inhibitors that are major components of the eukaryotic immune system. Pathogenic and colonizing bacteria, such as the opportunistic pathogen Pseudomonas aeruginosa, also carry structural homologs of eukaryotic A2Ms. Two types of bacterial A2Ms have been identified: Type I, much like the eukaryotic form, displays a conserved thioester that is essential for protease targeting, and Type II, which lacks the thioester and to date has been poorly studied despite its ubiquitous presence in Gram-negatives...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322448/characterization-of-circular-rnas-circrna-associated-with-the-translation-machinery
#11
Deniz Bartsch, Anne Zirkel, Leo Kurian
A substantial proportion of the currently annotated genes in eukaryotes are proposed to function as RNA molecules (>200 bp) with no significant protein coding potential, currently classified as long noncoding RNAs (lncRNA). A distinct subgroup of lncRNAs is circular RNAs (circRNAs), which can be easily identified by unique junction reads, resulting from their biogenesis. CircRNAs are largely cytosolic and thought to either code for micro-peptides or facilitate gene regulation by sequestering microRNAs (miRNAs) or RNA-binding proteins (RBPs) from their targets...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29321648/comparative-analysis-of-mirna-expression-profiles-in-transgenic-and-non-transgenic-rice-using-mirna-seq
#12
Cheng Peng, Xiaoyun Chen, Xiaofu Wang, Xiaoli Xu, Wei Wei, Congmao Wang, Junfeng Xu
Safety assessment for genetically modified organisms (GMOs) is required before their release. To date, miRNAs that play important roles in eukaryotic gene regulation have not been considered in the current assessment system. In this study, we identified 6 independent Bt and EPSPS GM rice lines using PCR and immune strip. We analyzed the expression levels of Cry1Ac and EPSPS using quantitative real-time PCR and western blot. Further, miRNAs from the developing seeds of the 6 GM rice lines and the wild-type line were investigated using deep sequencing and bioinformatic approaches...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29320490/the-glutamine-synthetase-of-trypanosoma-cruzi-is-required-for-its-resistance-to-ammonium-accumulation-and-evasion-of-the-parasitophorous-vacuole-during-host-cell-infection
#13
Marcell Crispim, Flávia Silva Damasceno, Agustín Hernández, María Julia Barisón, Ismael Pretto Sauter, Raphael Souza Pavani, Alexandre Santos Moura, Elizabeth Mieko Furusho Pral, Mauro Cortez, Maria Carolina Elias, Ariel Mariano Silber
Trypanosoma cruzi, the etiological agent of Chagas disease, consumes glucose and amino acids depending on the environmental availability of each nutrient during its complex life cycle. For example, amino acids are the major energy and carbon sources in the intracellular stages of the T. cruzi parasite, but their consumption produces an accumulation of NH4+ in the environment, which is toxic. These parasites do not have a functional urea cycle to secrete excess nitrogen as low-toxicity waste. Glutamine synthetase (GS) plays a central role in regulating the carbon/nitrogen balance in the metabolism of most living organisms...
January 10, 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29317511/exploration-of-the-germline-genome-of-the-ciliate-chilodonella-uncinata-through-single-cell-omics-transcriptomics-and-genomics
#14
Xyrus X Maurer-Alcalá, Rob Knight, Laura A Katz
Separate germline and somatic genomes are found in numerous lineages across the eukaryotic tree of life, often separated into distinct tissues (e.g., in plants, animals, and fungi) or distinct nuclei sharing a common cytoplasm (e.g., in ciliates and some foraminifera). In ciliates, germline-limited (i.e., micronuclear-specific) DNA is eliminated during the development of a new somatic (i.e., macronuclear) genome in a process that is tightly linked to large-scale genome rearrangements, such as deletions and reordering of protein-coding sequences...
January 9, 2018: MBio
https://www.readbyqxmd.com/read/29316898/inhibition-of-p38-mapk-activity-leads-to-cell-type-specific-effects-on-the-molecular-circadian-clock-and-time-dependent-reduction-of-glioma-cell-invasiveness
#15
Charles S Goldsmith, Sam Moon Kim, Nirmala Karunarathna, Nichole Neuendorff, L Gerard Toussaint, David J Earnest, Deborah Bell-Pedersen
BACKGROUND: The circadian clock is the basis for biological time keeping in eukaryotic organisms. The clock mechanism relies on biochemical signaling pathways to detect environmental stimuli and to regulate the expression of clock-controlled genes throughout the body. MAPK signaling pathways function in both circadian input and output pathways in mammals depending on the tissue; however, little is known about the role of p38 MAPK, an established tumor suppressor, in the mammalian circadian system...
January 10, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29316330/rna-seq-highlights-high-clonal-variation-in-monoclonal-antibody-producing-cho-cells
#16
Camila A Orellana, Esteban Marcellin, Robin W Palfreyman, Trent P Munro, Peter P Gray, Lars K Nielsen
The development of next-generation sequencing technologies has opened new opportunities to better characterize complex eukaryotic cells. Chinese hamster ovary (CHO) cells play a primary role in therapeutic protein production, with currently five of the top ten blockbuster drugs produced in CHO. However, engineering superior CHO cells with improved production features has had limited success to date and cell lines are still developed through the generation and screening of large strain pools. Here, we applied RNA sequencing to contrast a high and a low monoclonal antibody producing cell line...
January 5, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29315918/a-peroxisomal-thioesterase-plays-auxiliary-roles-in-plant-%C3%AE-oxidative-benzoic-acid-metabolism
#17
Funmilayo Adebesin, Joshua R Widhalm, Joseph H Lynch, Rachel M McCoy, Natalia Dudareva
Peroxisomal β-oxidative degradation of compounds is a common metabolic theme in eukaryotes. Reported benzoyl-CoA (BA-CoA) thioesterase activity in peroxisomes from petunia flowers suggests that, like mammals and fungi, plants contain auxiliary enzymes mediating β-oxidation. Here, we report identification of Petunia hybrida Thioesterase 1 (PhTE1), which catalyzes hydrolysis of aromatic acyl-CoAs to their corresponding acids in peroxisomes. PhTE1 expression is spatially, developmentally and temporally regulated and exhibits a similar pattern to known benzenoid metabolic genes...
January 6, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29313662/existence-of-internal-n7-methylguanosine-modification-in-mrna-determined-by-differential-enzyme-treatment-coupled-with-mass-spectrometry-analysis
#18
Jie-Mei Chu, Tian-Tian Ye, Cheng-Jie Ma, Meng-Dan Lan, Ting Liu, Bi-Feng Yuan, Yu-Qi Feng
The recent discovery of reversible chemical modifications on messenger RNA (mRNA) has opened a new era of post-transcriptional gene regulation in eukaryotes. Among the 15 types of modifications identified in mRNA of eukaryotes, N7-methylguanosine (m7G) is unique ow-ing to its presence in the 5' cap structure. It remains unknown whether m7G is also present in-ternally in mRNA, and this is largely attributed to the lack of an appropriate analytical method to differentiate internal m7G in mRNA from that in the 5' cap...
January 9, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29311343/the-interplay-between-the-rna-decay-and-translation-machinery-in-eukaryotes
#19
Adam M Heck, Jeffrey Wilusz
RNA decay plays a major role in regulating gene expression and is tightly networked with other aspects of gene expression to effectively coordinate post-transcriptional regulation. The goal of this work is to provide an overview of the major factors and pathways of general messenger RNA (mRNA) decay in eukaryotic cells, and then discuss the effective interplay of this cytoplasmic process with the protein synthesis machinery. Given the transcript-specific and fluid nature of mRNA stability in response to changing cellular conditions, understanding the fundamental networking between RNA decay and translation will provide a foundation for a complete mechanistic understanding of this important aspect of cell biology...
January 8, 2018: Cold Spring Harbor Perspectives in Biology
https://www.readbyqxmd.com/read/29305503/elucidating-waterborne-pathogen-presence-and-aiding-source-apportionment-in-an-impaired-stream
#20
Jennifer Weidhaas, Angela Anderson, Rubayat Jamal
Fecal indicator bacteria (FIB) are the basis for water quality regulations and are considered proxies for waterborne pathogens when conducting human health risk assessments. Direct detection of pathogens in water and simultaneous identification of the source of fecal contamination is possible with microarrays, circumventing drawbacks to FIB approaches. A multi-gene target microarray was used to assess the prevalence of waterborne pathogens in a fecally impaired, mixed use watershed. Results indicate that fecal coliforms have improved substantially in the watershed since its listing as a 303(d) impaired stream in 2002 and are now near United States recreational water criteria standards...
January 5, 2018: Applied and Environmental Microbiology
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