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https://www.readbyqxmd.com/read/28650559/the-antibacterial-activity-and-modes-of-li-f-type-antimicrobial-peptides-against-bacillus-cereus-in-vitro
#1
Jinzhi Han, Shengming Zhao, Zhi Ma, Ling Gao, Hongxia Liu, Umair Muhammad, Zhaoxin Lu, Fengxia Lv, Xiaomei Bie
AIMS: LI-Fs are a family of highly potent cyclic lipodepsipeptide antibiotics with a broad antimicrobial spectrum (Gram-positive bacteria and fungi). In this study, LI-F type antimicrobial peptides (AMP-jsa9) composing of LI-F03a, LI-F03b, LI-F04a, LI-F04b, and LI-F05b were isolated from Paenibacillus polymyxa JSA-9. To better understand the antimicrobial mechanism of AMP-jsa9, the potency and action(s) of AMP-jsa9 against B. cereus were examined. METHODS AND RESULTS: Flow cytometry, confocal laser microscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM), and atomic force microscopy (AFM) observation, as well as determination of peptidoglycan and cell wall associated protein, and other methods were used...
June 26, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28650470/signaling-coupled-epigenomic-regulation-of-gene-expression
#2
REVIEW
R Kumar, S Deivendran, T R Santhoshkumar, M R Pillai
Inheritance of genomic information independent of the DNA sequence, the epigenetics, as well as gene transcription are profoundly shaped by serine/threonine and tyrosine signaling kinases and components of the chromatin remodeling complexes. To precisely respond to a changing external milieu, human cells efficiently translate upstream signals into post-translational modifications (PTMs) on histones and coregulators such as corepressors, coactivators, DNA-binding factors and PTM modifying enzymes. Because a protein with multiple residues for putative PTMs is expected to undergo more than one PTM in cells stimulated with growth factors, the outcome of combinational PTM codes on histones and coregulators is profoundly shaped by regulatory interplays between PTMs...
June 26, 2017: Oncogene
https://www.readbyqxmd.com/read/28650145/the-dead-box-protein-cyt-19-uses-arginine-residues-in-its-c-tail-to-tether-rna-substrates
#3
Veronica F Busa, Maxwell J Rector, Rick Russell
DEAD-box proteins are nonprocessive RNA helicases that play diverse roles in cellular processes. The Neurospora crassa DEAD-box protein CYT-19 promotes mitochondrial group I intron splicing and functions as a general RNA chaperone. CYT-19 includes a disordered, arginine-rich 'C-tail' that binds RNA, positioning the helicase core to capture and unwind nearby RNA helices. Here we probed the C-tail further by varying the number and positions of arginines within it. We found that removing sets of as few as four of the eleven arginines reduced RNA unwinding activity (kcat/KM) equivalently to removing the C-tail, suggesting that a minimum or 'threshold' number of arginines is required...
June 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28649985/attenuation-of-rna-polymerase-ii-pausing-mitigates-brca1-associated-r-loop-accumulation-and-tumorigenesis
#4
Xiaowen Zhang, Huai-Chin Chiang, Yao Wang, Chi Zhang, Sabrina Smith, Xiayan Zhao, Sreejith J Nair, Joel Michalek, Ismail Jatoi, Meeghan Lautner, Boyce Oliver, Howard Wang, Anna Petit, Teresa Soler, Joan Brunet, Francesca Mateo, Miguel Angel Pujana, Elizabeth Poggi, Krysta Chaldekas, Claudine Isaacs, Beth N Peshkin, Oscar Ochoa, Frederic Chedin, Constantine Theoharis, Lu-Zhe Sun, Tyler J Curiel, Richard Elledge, Victor X Jin, Yanfen Hu, Rong Li
Most BRCA1-associated breast tumours are basal-like yet originate from luminal progenitors. BRCA1 is best known for its functions in double-strand break repair and resolution of DNA replication stress. However, it is unclear whether loss of these ubiquitously important functions fully explains the cell lineage-specific tumorigenesis. In vitro studies implicate BRCA1 in elimination of R-loops, DNA-RNA hybrid structures involved in transcription and genetic instability. Here we show that R-loops accumulate preferentially in breast luminal epithelial cells, not in basal epithelial or stromal cells, of BRCA1 mutation carriers...
June 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28649752/investigating-dna-rna-and-protein-based-features-as-a-means-to-discriminate-pathogenic-synonymous-variants
#5
Mark Livingstone, Lukas Folkman, Yuedong Yang, Ping Zhang, Matthew Mort, David N Cooper, Yunlong Liu, Bela Stantic, Yaoqi Zhou
Synonymous single nucleotide variants (SNVs), although they do not alter the encoded protein sequences, have been implicated in many genetic diseases. Experimental studies indicate that synonymous SNVs can lead to changes in the secondary and tertiary structures of DNA and RNA, thereby impacting translational efficiency, co-translational protein folding as well as the binding of DNA/RNA-binding proteins. However, the importance of these various features in disease phenotypes is not clearly understood. Here we have built a support vector machine model (termed DDIG-SN) as a means to discriminate disease-causing synonymous variants...
June 25, 2017: Human Mutation
https://www.readbyqxmd.com/read/28649742/genotranscriptomic-meta-analysis-of-the-chd-family-chromatin-remodelers-in-human-cancers-initial-evidence-of-an-oncogenic-role-for-chd7
#6
Xiaofang Chu, Xuhui Guo, Yuanyuan Jiang, Huimei Yu, Lanxin Liu, Wenqi Shan, Zeng-Quan Yang
Chromodomain helicase DNA binding proteins (CHD) are characterized by N-terminal tandem chromodomains and a central ATP-dependent helicase domain. CHDs govern the cellular machinery's access to DNA, thereby playing critical roles in various cellular processes including transcription, proliferation, and DNA damage repair. Accumulating evidence demonstrates that mutation and dysregulation of CHDs are implicated in the pathogenesis of developmental disorders and cancer. However, we know little about genomic and transcriptomic alterations and the clinical significance of most CHDs in human cancer...
June 26, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28649584/data-for-characterization-of-salk_084889-a-t-dna-insertion-line-of-arabidopsis-thaliana
#7
Mingqi Zhou, Anna-Lisa Paul, Robert J Ferl
In this article we report the identification of T-DNA (transfer DNA) insertion sites within two different gene regions in the genome of an Arabidopsis mutant line, SALK_084889. The T-DNA positions are in the 3' UTR (untranslated region) of DREB2A (Dehydration-responsive element-binding protein 2A) (AT5G05410) and promoter of LOX1 (Lipoxygenase 1) (AT1G55020) as determined by DNA-PCR and sanger sequencing. The expression levels of DREB2A and LOX1 were also analyzed using quantitative realtime PCR (qPCR) in SALK_084889 and wild type Arabidopsis (Col, Columbia)...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28649093/ntl8-regulates-trichome-formation-in-arabidopsis-by-directly-activating-r3-myb-genes-try-and-tcl1
#8
Hainan Tian, Xianling Wang, Hongyan Guo, Yuxin Cheng, Chunjiang Hou, Jin-Gui Chen, Shucai Wang
The NAM, ATAF1/2, and CUC (NAC) are plant-specific transcription factors that regulate multiple aspects of plant growth and development, and plant response to environmental stimuli. We report here the identification of NTM1-LIKE 8 (NTL8), a membrane-associated NAC transcription factor, as a novel regulator of trichome formation in Arabidopsis. From an activation-tagged Arabidopsis population, we identified a dominant, gain-of-function mutant with glabrous inflorescence stem. By using plasmid rescue and RT-PCR analyses, we found that NTL8 was tagged, thus the mutant was named ntl8-1 Dominant (ntl8-1D)...
June 25, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28648678/single-plane-illumination-microscopy-as-a-tool-for-studying-nucleome-dynamics
#9
Jörg Langowski
Single plane illumination microscopy (SPIM) is a new optical method that has become extremely important in recent years. It is based on the formation of a "light slice" in the specimen in which fluorescently tagged molecules are observed. The spatial resolution is close to that of confocal optics, but without the disadvantages inherent to scanning or high laser irradiation doses. A recent development is light sheet fluctuation microscopy, which exploits the dynamic information contained in the fluorescence intensity fluctuations of each image pixel...
June 22, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28647366/crystal-structure-of-the-crenarchaeal-exoiii-ap-endonuclease-sisexoiii-reveals-a-conserved-disulfide-bond-endowing-the-protein-with-thermostability
#10
Zhou Yan, Zenglin Yuan, Jinfeng Ni, Lichuan Gu, Yulong Shen
AP endonuclease recognizes and cleaves apurinic/apyrimidinic (AP) sites and plays a critical role in base excision repair. Many ExoIII and EndoIV family AP endonucleases have been characterized both biochemically and structurally in Eukaryote and Bacteria. However, relatively fewer have been studied in Euryarchaeota and there is no such report on an AP endonuclease from Crenarchaeota. Here we report, for the first time, the crystal structure of a crenarchaeal ExoIII AP endonuclease, SisExoIII, from Sulfolobus islandicus REY15A...
June 21, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28647120/drrc-protein-of-streptomyces-peucetius-removes-daunorubicin-from-intercalated-dnri-promoter
#11
Francis Prija, Ranjan Prasad
DrrC is a DNA-binding protein of Streptomyces peucetius that provides self-resistance against daunorubicin, the antibiotic produced by the organism. DrrC was expressed in E.coli and purified by using N-terminal MBP-tag which retained DNA-binding property in spite of the tag. Mobility shift assay confirmed the interaction of 313bp DNA that has the dnrI promoter, daunorubicin and MBP-DrrC in the presence of ATP. Biotinylated and immobilized 313bp DNA was intercalated with daunorubicin to observe the release of the drug when MBP-DrrC is allowed to act on the DNA...
September 2017: Microbiological Research
https://www.readbyqxmd.com/read/28646552/targeting-histone-deacetylase-4-ubc9-impairs-dna-repair-for-radiosensitization-of-hepatocellular-carcinoma-cells
#12
Chiao-Ling Tsai, Wei-Lin Liu, Feng-Ming Hsu, Po-Sheng Yang, Ruoh-Fang Yen, Kai-Yuan Tzen, Ann-Lii Cheng, Pei-Jer Chen, Jason Chia-, Hsien Cheng
Several strategies to improve the efficacy of radiation therapy against hepatocellular carcinoma (HCC) have been investigated. One approach was to develop radiosensitizing compounds. Because histone deacetylase 4 (HDAC4) is highly expressed in liver cancer and known to regulate oncogenesis through chromatin structure remodeling and controlling protein access to DNA, we postulated that HDAC4 inhibition might enhance radiation's effect on HCC cells. HCC cell lines (Huh7 and PLC5) and an ectopic xenograft were pretreated with HDAC inhibitor or shRNA to knock down expression of HDAC4, and then irradiated (2...
June 23, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28646284/chd1l-expression-increases-tumor-progression-and-acts-as-a-predictive-biomarker-for-poor-prognosis-in-pancreatic-cancer
#13
Chuan Liu, Xiaowei Fu, Zhiwei Zhong, Jing Zhang, Haiyan Mou, Qiong Wu, Tianle Sheng, Bo Huang, Yeqing Zou
BACKGROUND: The chromodomain helicase/ATPase DNA binding protein 1-like gene (CHD1L) plays a key role in controlling various cellular phenomena, including immune-mediated inflammation, transformation, apoptosis, cell cycle progression, and proliferation. METHODS: This study investigated the function and clinical significance of CHD1L protein expression in pancreatic cancer (PC). We analyzed CHD1L expression in surgical specimens from 112 PC patients. The correlation between the clinical characteristics and prognosis was also determined...
June 23, 2017: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/28646110/the-mcm2-7-interacting-domain-of-human-mini-chromosome-maintenance-10-mcm10-protein-is-important-for-stable-chromatin-association-and-origin-firing
#14
Masako Izumi, Takeshi Mizuno, Ken-Ichiro Yanagi, Kazuto Sugimura, Katsuzumi Okumura, Naoko Imamoto, Tomoko Abe, Fumio Hanaoka
The protein mini-chromosome maintenance 10 (Mcm10) was originally identified as an essential yeast protein in the maintenance of mini-chromosome plasmids. Subsequently, Mcm10 has been shown to be required for both initiation and elongation during chromosomal DNA replication. However, it is not fully understood how the multiple functions of Mcm10 are coordinated or how Mcm10 interacts with other factors at replication forks. Here, we identified and characterized the Mcm2-7-interacting domain in human Mcm10. The interaction with Mcm2-7 required the Mcm10 domain that contained amino acids 530-655, which overlapped with the domain required for the stable retention of Mcm10 on chromatin...
June 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28645917/multivalent-binding-of-pwwp2a-to-h2a-z-regulates-mitosis-and-neural-crest-differentiation
#15
Sebastian Pünzeler, Stephanie Link, Gabriele Wagner, Eva C Keilhauer, Nina Kronbeck, Ramona Mm Spitzer, Susanne Leidescher, Yolanda Markaki, Edith Mentele, Catherine Regnard, Katrin Schneider, Daisuke Takahashi, Masayuki Kusakabe, Chiara Vardabasso, Lisa M Zink, Tobias Straub, Emily Bernstein, Masahiko Harata, Heinrich Leonhardt, Matthias Mann, Ralph Aw Rupp, Sandra B Hake
Replacement of canonical histones with specialized histone variants promotes altering of chromatin structure and function. The essential histone variant H2A.Z affects various DNA-based processes via poorly understood mechanisms. Here, we determine the comprehensive interactome of H2A.Z and identify PWWP2A as a novel H2A.Z-nucleosome binder. PWWP2A is a functionally uncharacterized, vertebrate-specific protein that binds very tightly to chromatin through a concerted multivalent binding mode. Two internal protein regions mediate H2A...
June 23, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28645570/quantitative-proteomics-analysis-by-itraq-revealed-underlying-changes-in-thermotolerance-of-arthrospira-platensis
#16
Rong Chang, Bingxin Lv, Bosheng Li
Growth temperature is a critical factor that affects cultivation of Arthrospira platensis which is a type of cyanobacterium widely known as Spirulina that has significant commercial value. To investigate the molecular mechanism underlying the thermotolerance of Spirulina, differential protein expression profiling was carried out using iTRAQ-based quantitative proteomic analysis. This study only analyzed changes in thylakoids. Among the 2085 proteins quantified, 43 differentially expressed proteins were selected based on the fold change cutoff scores of ≥2 or ≤0...
June 20, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28645377/electrical-probes-of-dna-binding-proteins
#17
Jacqueline K Barton, Phillip L Bartels, Yingxin Deng, Elizabeth O'Brien
A DNA electrochemistry platform has been developed to probe proteins bound to DNA electrically. Here gold electrodes are modified with thiol-modified DNA, and DNA charge transport chemistry is used to probe DNA binding and enzymatic reaction both with redox-silent and redox-active proteins. For redox-active proteins, the electrochemistry permits the determination of redox potentials in the DNA-bound form, where comparisons to DNA-free potentials can be made using graphite electrodes without DNA modification...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28645321/genome-wide-analysis-of-dna-methylation-in-hypothalamus-and-ovary-of-capra-hircus
#18
Stefano Frattini, Emanuele Capra, Barbara Lazzari, Stephanie D McKay, Beatrice Coizet, Andrea Talenti, Debora Groppetti, Pietro Riccaboni, Alessandro Pecile, Stefania Chessa, Bianca Castiglioni, John L Williams, Giulio Pagnacco, Alessandra Stella, Paola Crepaldi
BACKGROUND: DNA methylation is a frequently studied epigenetic modification due to its role in regulating gene expression and hence in biological processes and in determining phenotypic plasticity in organisms. Rudimentary DNA methylation patterns for some livestock species are publically available: among these, goat methylome deserves to be further explored. RESULTS: Genome-wide DNA methylation maps of the hypothalamus and ovary from Saanen goats were generated using Methyl-CpG binding domain protein sequencing (MBD-seq)...
June 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28645209/genome-wide-mapping-of-in-vivo-er%C3%AE-binding-sites-in-male-mouse-efferent-ductules
#19
Guangxin Yao, Shuanggang Hu, Lu Yu, Yanfei Ru, Charlie Degui Chen, Qiang Liu, Yonglian Zhang
As an important nuclear hormone receptor, estrogen receptor alpha (ERα), which is encoded by Esr1 gene, regulates the expression of hundreds of genes in a stimulus-specific, temporal and tissue-specific fashion, mainly by binding to specific DNA sequences-estrogen response elements (EREs). As an important estrogen target tissue in males, the function of the efferent ductules relies on the presence of the ERα protein, but the underlying regulatory mechanisms are poorly illustrated. In this study, genome-wide ERα-binding sites in mouse efferent ductules were mapped by ChIP-seq...
June 22, 2017: Endocrinology
https://www.readbyqxmd.com/read/28645103/colxv-promotes-adipocyte-differentiation-via-inhibiting-dna-methylation-and-camp-pka-pathway-in-mice
#20
Guannv Liu, Meihang Li, Yatao Xu, Song Wu, Muhammad Saeed, Chao Sun
Extracellular matrix (ECM), as an essential component of adipose tissue, not only provides mechanical support for adipocyte growth, but also participates in ECM-adipocyte communication via various secreted proteins, including highly enriched collagens. Collagen XV (ColXV) is a secreted non-fibrillar collagen within ECM Basement Membrane (BM) zones and well recognized as a tumor suppressor. However, the role of ColXV in adipose tissue is still unknown. In this study, high fat diet (HFD) fed mice were used as obese model, in which we deeply investigated the interaction between ColXV and adipocyte differentiation or adipose metabolism...
June 16, 2017: Oncotarget
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