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https://www.readbyqxmd.com/read/28087277/identification-of-ubact-a-ubiquitin-like-protein-along-with-other-homologous-components-of-a-conjugation-system-and-the-proteasome-in-different-gram-negative-bacteria
#1
Gilad Lehmann, Ronald G Udasin, Ido Livneh, Aaron Ciechanover
Systems analogous to the eukaryotic ubiquitin-proteasome system have been previously identified in Archaea, and Actinobacteria (gram-positive), but not in gram-negative bacteria. Here, we report the bioinformatic identification of a novel prokaryotic ubiquitin-like protein, which we name UBact. The phyletic distribution of UBact covers at least five gram-negative bacterial phyla, including Nitrospirae, Armatimonadetes, Verrucomicroba, Nitrospinae, and Planctomycetes. Additionally, it was identified in seven candidate (uncultured) phyla and one Archaeon...
January 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28087276/drosophila-argonaute2-turnover-is-regulated-by-the-ubiquitin-proteasome-pathway
#2
Madoka Chinen, Elissa P Lei
Argonaute (AGO) proteins play a central role in the RNA interference (RNAi) pathway, which is a cytoplasmic mechanism important for post-transcriptional regulation of gene expression. In Drosophila, AGO2 also functions in the nucleus to regulate chromatin insulator activity and transcription. Although there are a number of studies focused on AGO2 function, the regulation of AGO2 turnover is not well understood. We found that mutation of T1149 or R1158 in the conserved PIWI domain causes AGO2 protein instability, but only T1149 affects RNAi activity...
January 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28079229/the-transcription-factor-xbp1-in-memory-and-cognition-implications-in-alzheimer-disease
#3
Moustapha Cissé, Eric Duplan, Frédéric Checler
X-box binding protein 1 (XBP1) is a unique basic region leucine zipper transcription factor isolated two decades ago in a search for regulators of major histocompatibility complex class II gene expression. XBP1 is a very complex protein regulating many physiological functions, including immune system, inflammatory responses, and lipid metabolism. Evidence over the past few years suggests that XBP1 also plays important roles in pathological settings since its activity as transcription factor has profound effects on the prognosis and progression of diseases such as cancer, neurodegeneration, and diabetes...
January 4, 2017: Molecular Medicine
https://www.readbyqxmd.com/read/28077607/anatomy-of-mdm2-and-mdm4-in-evolution
#4
REVIEW
Ban Xiong Tan, Hoe Peng Liew, Joy S Chua, Farid J Ghadessy, Yaw Sing Tan, David P Lane, Cynthia R Coffill
Mouse double minute (Mdm) genes span an evolutionary timeframe from the ancient eukaryotic placozoa Trichoplax adhaerens to Homo sapiens, implying a significant and possibly conserved cellular role throughout history. Maintenance of DNA integrity and response to DNA damage involve many key regulatory pathways, including precise control over the tumour suppressor protein p53. In most vertebrates, degradation of p53 through proteasomal targeting is primarily mediated by heterodimers of Mdm2 and the Mdm2-related protein Mdm4 (also known as MdmX)...
January 10, 2017: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/28067168/sumoylation-in-neurological-diseases
#5
F-Y Liu, Y-F Liu, Y Yang, Z-W Luo, J-W Xiang, Z-G Chen, R-L Qi, T-H Yang, Y Xiao, W-J Qing, D W-C Li
Since the discovery of SUMOs (small ubiquitin-like modifiers) over 20 years ago, sumoylation has recently emerged as an important post-translational modification involved in almost all aspects of cellular physiology. In neurons, sumoylation dynamically modulates protein function and consequently plays an important role in neuronal maturation, synapse formation and plasticity. Thus, the dysfunction of sumoylation pathway is associated with many different neurological disorders. Hundreds of different proteins implicated in the pathogenesis of neurological disorders are SUMO-modified, indicating the importance of sumoylation involved in the neurological diseases...
January 9, 2017: Current Molecular Medicine
https://www.readbyqxmd.com/read/28065316/single-molecule-measurements-to-study-polymerization-dynamics-of-ftsz-ftsa-copolymers
#6
N Baranova, M Loose
Bacterial cytokinesis is commonly initiated by the Z-ring, a dynamic cytoskeletal structure that assembles at the site of division. Its primary component is FtsZ, a tubulin-like GTPase, that like its eukaryotic relative forms protein filaments in the presence of GTP. Since the discovery of the Z-ring 25years ago, various models for the role of FtsZ have been suggested. However, important information about the architecture and dynamics of FtsZ filaments during cytokinesis is still missing. One reason for this lack of knowledge has been the small size of bacteria, which has made it difficult to resolve the orientation and dynamics of individual FtsZ filaments in the Z-ring...
2017: Methods in Cell Biology
https://www.readbyqxmd.com/read/28062044/multiplexed-tethered-particle-microscopy-for-studies-of-dna-enzyme-dynamics
#7
S Ucuncuoglu, D A Schneider, E R Weeks, D Dunlap, L Finzi
DNA is the carrier of genetic information and, as such, is at the center of most essential cellular processes. To regulate its physiological function, specific proteins and motor enzymes constantly change conformational states with well-controlled dynamics. Twenty-five years ago, Schafer, Gelles, Sheetz, and Landick employed the tethered particle motion (TPM) technique for the first time to study transcription by RNA polymerase at the single-molecule level. TPM has since then remained one of the simplest, most affordable, and yet incisive single-molecule techniques available...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28061688/aptamers-as-therapeutics
#8
Shahid M Nimjee, Rebekah R White, Richard C Becker, Bruce A Sullenger
Aptamers are single-stranded nucleic acid molecules that bind to and inhibit proteins and are commonly produced by systematic evolution of ligands by exponential enrichment (SELEX). Aptamers undergo extensive pharmacological revision, which alters affinity, specificity, and therapeutic half-life, tailoring each drug for a specific clinical need. The first therapeutic aptamer was described 25 years ago. Thus far, one aptamer has been approved for clinical use, and numerous others are in preclinical or clinical development...
January 6, 2017: Annual Review of Pharmacology and Toxicology
https://www.readbyqxmd.com/read/28060488/aminoacyl-trna-utilizing-enzymes-in-natural-product-biosynthesis
#9
Mireille Moutiez, Pascal Belin, Muriel Gondry
Aminoacyl-tRNAs were long thought to be involved solely in ribosome-dependent protein synthesis and essential primary metabolism processes, such as targeted protein degradation and peptidoglycan synthesis. About 10 years ago, an aminoacyl-tRNA-dependent enzyme involved in the biosynthesis of the antibiotic valanimycin was discovered in a Streptomyces strain. Far from being an isolated case, this discovery has been followed by the description of an increasing number of aminoacyl-tRNA-dependent enzymes involved in secondary metabolism...
January 6, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28059073/ros-accumulation-and-antiviral-defence-control-by-microrna528-in-rice
#10
Jianguo Wu, Rongxin Yang, Zhirui Yang, Shengze Yao, Shanshan Zhao, Yu Wang, Pingchuan Li, Xianwei Song, Lian Jin, Tong Zhou, Ying Lan, Lianhui Xie, Xueping Zhou, Chengcai Chu, Yijun Qi, Xiaofeng Cao, Yi Li
MicroRNAs (miRNAs) are key regulators of plant-pathogen interactions. Modulating miRNA function has emerged as a new strategy to produce virus resistance traits(1-5). However, the miRNAs involved in antiviral defence and the underlying mechanisms remain largely elusive. We previously demonstrated that sequestration by Argonaute (AGO) proteins plays an important role in regulating miRNA function in antiviral defence pathways(6). Here we reveal that cleavage-defective AGO18 complexes sequester microRNA528 (miR528) upon viral infection...
January 6, 2017: Nature Plants
https://www.readbyqxmd.com/read/28053006/co-option-and-de-novo-gene-evolution-underlie-molluscan-shell-diversity
#11
Felipe Aguilera, Carmel McDougall, Bernard M Degnan
Molluscs fabricate shells of incredible diversity and complexity by localized secretions from the dorsal epithelium of the mantle. Although distantly-related molluscs express remarkably different secreted gene products, it remains unclear if the evolution of shell structure and pattern is underpinned by the differential co-option of conserved genes or the integration of lineage-specific genes into the mantle regulatory program. To address this, we compare the mantle transcriptomes of 11 bivalves and gastropods of varying relatedness...
January 4, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28046132/transcriptome-wide-discovery-of-pasrs-promoter-associated-small-rnas-and-tasrs-terminus-associated-small-rnas-in-arabidopsis-thaliana
#12
Xiaoxia Ma, Ning Han, Chaogang Shao, Yijun Meng
Hints from animals point to the existence of two novel small RNA (sRNA) species surrounding the transcription start sites (TSSs) and the termini of the genes, respectively. In this study, we performed a comprehensive search for the two sRNA species named promoter-associated sRNAs (PASRs) and terminus-associated sRNAs (TASRs) in Arabidopsis. By using sRNA sequencing data from wild type plants and several mutants related to the sRNA biogenesis, Argonaute (AGO) 1- and AGO4-associated sRNA sequencing data, double-stranded RNA sequencing (dsRNA-seq) data, and DNA methylation profiling data, the biogenesis and action pathways of the PASRs and the TASRs were investigated...
2017: PloS One
https://www.readbyqxmd.com/read/28040746/sixty-five-years-of-the-long-march-in-protein-secondary-structure-prediction-the-final-stretch
#13
Yuedong Yang, Jianzhao Gao, Jihua Wang, Rhys Heffernan, Jack Hanson, Kuldip Paliwal, Yaoqi Zhou
Protein secondary structure prediction began in 1951 when Pauling and Corey predicted helical and sheet conformations for protein polypeptide backbone even before the first protein structure was determined. Sixty-five years later, powerful new methods breathe new life into this field. The highest three-state accuracy without relying on structure templates is now at 82-84%, a number unthinkable just a few years ago. These improvements came from increasingly larger databases of protein sequences and structures for training, the use of template secondary structure information and more powerful deep learning techniques...
December 31, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28039969/classical-investigation-of-long-range-coherence-in-biological-systems
#14
Jordane Preto
Almost five decades ago, H. Fröhlich [H. Fröhlich, "Long-range coherence and energy storage in biological systems," Int. J. Quantum Chem. 2(5), 641-649 (1968)] reported, on a theoretical basis, that the excitation of quantum modes of vibration in contact with a thermal reservoir may lead to steady states, where under high enough rate of energy supply, only specific low-frequency modes of vibration are strongly excited. This nonlinear phenomenon was predicted to occur in biomolecular systems, which are known to exhibit complex vibrational spectral properties, especially in the terahertz frequency domain...
December 2016: Chaos
https://www.readbyqxmd.com/read/28039401/smoking-correlates-with-increased-cytoskeletal-protein-related-coding-region-mutations-in-the-lung-and-head-and-neck-datasets-of-the-cancer-genome-atlas
#15
John M Yavorski, George Blanck
Cancer from smoking tobacco is considered dependent on mutagens, but significant molecular aspects of smoking-specific, cancer development remain unknown. We defined sets of coding regions for oncoproteins, tumor suppressor proteins, and cytoskeletal-related proteins that were compared between nonsmokers and smokers, for mutation occurrences, in the lung adenocarcinoma (LUAD), head and neck squamous carcinoma (HNSC), bladder carcinoma (BLCA), and pancreatic adenocarcinoma ( PAAD) datasets from the cancer genome atlas (TCGA)...
December 2016: Physiological Reports
https://www.readbyqxmd.com/read/28039207/nup358-binds-to-ago-proteins-through-its-sumo-interacting-motifs-and-promotes-the-association-of-target-mrna-with-mirisc
#16
Manas Ranjan Sahoo, Swati Gaikwad, Deepak Khuperkar, Maitreyi Ashok, Mary Helen, Santosh Kumar Yadav, Aditi Singh, Indrasen Magre, Prachi Deshmukh, Supriya Dhanvijay, Pabitra Kumar Sahoo, Yogendra Ramtirtha, Mallur Srivatsan Madhusudhan, Pananghat Gayathri, Vasudevan Seshadri, Jomon Joseph
MicroRNA (miRNA)-guided mRNA repression, mediated by the miRNA-induced silencing complex (miRISC), is an important component of post-transcriptional gene silencing. However, how miRISC identifies the target mRNA in vivo is not well understood. Here, we show that the nucleoporin Nup358 plays an important role in this process. Nup358 localizes to the nuclear pore complex and to the cytoplasmic annulate lamellae (AL), and these structures dynamically associate with two mRNP granules: processing bodies (P bodies) and stress granules (SGs)...
December 30, 2016: EMBO Reports
https://www.readbyqxmd.com/read/28025543/rna-editing-and-its-molecular-mechanism-in-plant-organelles
#17
REVIEW
Mizuho Ichinose, Mamoru Sugita
RNA editing by cytidine (C) to uridine (U) conversions is widespread in plant mitochondria and chloroplasts. In some plant taxa, "reverse" U-to-C editing also occurs. However, to date, no instance of RNA editing has yet been reported in green algae and the complex thalloid liverworts. RNA editing may have evolved in early land plants 450 million years ago. However, in some plant species, including the liverwort, Marchantia polymorpha, editing may have been lost during evolution. Most RNA editing events can restore the evolutionarily conserved amino acid residues in mRNAs or create translation start and stop codons...
December 23, 2016: Genes
https://www.readbyqxmd.com/read/28017137/effects-of-crosstalk-between-sumoylation-and-phosphorylation-in-normal-cellular-physiology-and-human-diseases
#18
Q Nie, X-D Gong, M Liu, D W-C Li
Post-translational modifications (PTMs) such as phosphorylation, acetylation, methylation, ubiquitylation, sumoylation are important mechanisms to regulate the functions of different proteins. Among various PTMs, phosphorylation, discovered about 60 years ago, is probably the most common modification. In contrast, sumoylation, identified about two decades is emerging as a key regulatory mechanism modulating protein functions. Although studies on protein phosphorylation and sumoylation have been extensively reviewed, much less attention has been paid to their cross-talk and their co-regulation of the same protein target...
December 22, 2016: Current Molecular Medicine
https://www.readbyqxmd.com/read/28011975/dental-worm-disease
#19
Sergio Sabbatani, Sirio Fiorino
During human evolution, the period in which groups of humans stopped harvesting fruits and seeds growing wild and introduced the cultivation of cereals as well as the domestication of animals represents a very important event. This circumstance had a considerable impact on human pathocenosis, increasing the risk of infectious diseases of animal origin. The aim of this review was to summarise the archaeological and palaeo-pathological evidence in the literature concerning this topic. Starting from early prehistory (about 1...
1, 2016: Le Infezioni in Medicina
https://www.readbyqxmd.com/read/28011762/idh1-deficiency-attenuates-gluconeogenesis-in-mouse-liver-by-impairing-amino-acid-utilization
#20
Jing Ye, Yu Gu, Feng Zhang, Yuanlin Zhao, Yuan Yuan, Zhenyue Hao, Yi Sheng, Wanda Y Li, Andrew Wakeham, Rob A Cairns, Tak W Mak
Although the enzymatic activity of isocitrate dehydrogenase 1 (IDH1) was defined decades ago, its functions in vivo are not yet fully understood. Cytosolic IDH1 converts isocitrate to α-ketoglutarate (α-KG), a key metabolite regulating nitrogen homeostasis in catabolic pathways. It was thought that IDH1 might enhance lipid biosynthesis in liver or adipose tissue by generating NADPH, but we show here that lipid contents are relatively unchanged in both IDH1-null mouse liver and IDH1-deficient HepG2 cells generated using the CRISPR-Cas9 system...
December 23, 2016: Proceedings of the National Academy of Sciences of the United States of America
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