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https://www.readbyqxmd.com/read/30092083/pseudomonas-aeruginosa-nfua-gene-regulation-and-its-physiological-roles-in-sustaining-growth-under-stress-and-anaerobic-conditions-and-maintaining-bacterial-virulence
#1
Adisak Romsang, Jintana Duang-Nkern, Kritsakorn Saninjuk, Paiboon Vattanaviboon, Skorn Mongkolsuk
The role of the nfuA gene encoding an iron-sulfur ([Fe-S]) cluster-delivery protein in the pathogenic bacterium Pseudomonas aeruginosa was investigated. The analysis of nfuA expression under various stress conditions showed that superoxide generators, a thiol-depleting agent and CuCl2 highly induced nfuA expression. The expression of nfuA was regulated by a global [2Fe-2S] cluster containing the transcription regulator IscR. Increased expression of nfuA in the ΔiscR mutant under uninduced conditions suggests that IscR acts as a transcriptional repressor...
2018: PloS One
https://www.readbyqxmd.com/read/30082643/genome-wide-characterization-of-dna-demethylase-genes-and-their-association-with-salt-response-in-pyrus
#2
Chunxiao Liu, Hui Li, Jing Lin, Ying Wang, Xiaoyang Xu, Zong-Ming Max Cheng, Yonghong Chang
DNA methylation plays important roles in genome protection and the regulation of gene expression and it is associated with plants' responses to environments. DNA demethylases are very important proteins in DNA methylation regulation. In this study, we performed genome-wide and deep analysis of putative demethylases (DMEs) in pear. Seven DME genes were found in the pear genome and were defined as PbDME1⁻7 based on their domain organization. Results were supported by the gene structural characteristics and phylogenetic analysis...
August 6, 2018: Genes
https://www.readbyqxmd.com/read/29895158/characterization-of-a-new-genotype-of-betapapillomavirus-hpv-17-through-l1-e7-e7-and-lcr-sequences
#3
L Oliveira, L Santos, F Neves
Human papillomavirus (HPV) exhibits epithelial and mucosal tropism. HPV type 17 belongs to the Betapapillomavirus genus and molecular cloning experiments have identified two subtypes (17a and 17b) isolated from epidermodysplasia verruciformis (EV). HPV subtypes are characterized by dissimilarities from 2 to 10% at the nucleotide level from their referenced HPV. The aim of this study was to characterize the L1, E6, E7 and LCR sequences from an isolate, which was recovered from the oral mucosa of an asymptomatic 63 year-old woman...
2018: Acta Virologica
https://www.readbyqxmd.com/read/29760236/anti-%C3%AF-factor-ylad-regulates-transcriptional-activity-of-%C3%AF-factor-ylac-and-sporulation-via-manganese-dependent-redox-sensing-molecular-switch-in-bacillus-subtilis
#4
Min-Kyu Kwak, Han-Bong Ryu, Sung-Hyun Song, Jin-Won Lee, Sa-Ouk Kang
YlaD, a membrane-anchored anti-sigma (σ) factor of Bacillus subtilis , contains a HX3 CXXC motif that functions as a redox-sensing domain and belongs to one of the zinc (Zn)-co-ordinated anti-σ factor families. Despite previously showing that the YlaC transcription is controlled by YlaD, experimental evidence of how the YlaC-YlaD interaction is affected by active cysteines and/or metal ions is lacking. Here, we showed that the P yla promoter is autoregulated solely by YlaC. Moreover, reduced YlaD contained Zn and iron, while oxidized YlaD did not...
July 5, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29627878/discovery-of-a-small-molecule-inhibitor-of-dvl-cxxc5-interaction-by-computational-approaches
#5
Songling Ma, Jiwon Choi, Xuemei Jin, Hyun-Yi Kim, Ji-Hye Yun, Weontae Lee, Kang-Yell Choi, Kyoung Tai No
The Wnt/β-catenin signaling pathway plays a significant role in the control of osteoblastogenesis and bone formation. CXXC finger protein 5 (CXXC5) has been recently identified as a negative feedback regulator of osteoblast differentiation through a specific interaction with Dishevelled (Dvl) protein. It was reported that targeting the Dvl-CXXC5 interaction could be a novel anabolic therapeutic target for osteoporosis. In this study, complex structure of Dvl PDZ domain and CXXC5 peptide was simulated with molecular dynamics (MD)...
May 2018: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/29556496/tet-enzymes-variants-and-differential-effects-on-function
#6
REVIEW
Philippa Melamed, Yahav Yosefzon, Cfir David, Anna Tsukerman, Lilach Pnueli
Discovery of the ten-eleven translocation 1 (TET) methylcytosine dioxygenase family of enzymes, nearly 10 years ago, heralded a major breakthrough in understanding the epigenetic modifications of DNA. Initially described as catalyzing the oxidation of methyl cytosine (5mC) to hydroxymethyl cytosine (5hmC), it is now clear that these enzymes can also catalyze additional reactions leading to active DNA demethylation. The association of TET enzymes, as well as the 5hmC, with active regulatory regions of the genome has been studied extensively in embryonic stem cells, although these enzymes are expressed widely also in differentiated tissues...
2018: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29540477/the-cellular-stress-proteins-chchd10-and-mnrr1-chchd2-partners-in-mitochondrial-and-nuclear-function-and-dysfunction
#7
Neeraja Purandare, Mallika Somayajulu, Maik Hüttemann, Lawrence I Grossman, Siddhesh Aras
Coiled-coil-helix-coiled-coil-helix domain-containing 10 (CHCHD10) and CHCHD2 (MNRR1) are homologous proteins with 58% sequence identity and belong to the twin CX9 C family of proteins that mediate cellular stress responses. Despite the identification of several neurodegeneration-associated mutations in the CHCHD10 gene, few studies have assessed its physiological role. Here, we investigated CHCHD10's function as a regulator of oxidative phosphorylation in the mitochondria and the nucleus. We show that CHCHD10 copurifies with cytochrome c oxidase (COX) and up-regulates COX activity by serving as a scaffolding protein required for MNRR1 phosphorylation, mediated by ARG (ABL proto-oncogene 2, nonreceptor tyrosine kinase (ABL2))...
April 27, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29415182/arabidopsis-zinc-finger-like-protein-asymmetric-leaves2-as2-and-two-nucleolar-proteins-maintain-gene-body-dna-methylation-in-the-leaf-polarity-gene-ettin-arf3
#8
Simon Vial-Pradel, Sumie Keta, Mika Nomoto, Lilan Luo, Hiro Takahashi, Masataka Suzuki, Yuri Yokoyama, Michiko Sasabe, Shoko Kojima, Yasuomi Tada, Yasunori Machida, Chiyoko Machida
Arabidopsis ASYMMETRIC LEAVES2 (AS2) plays a critical role in leaf adaxial-abaxial partitioning by repressing expression of the abaxial-determining gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). We previously reported that six CpG dinucleotides in its exon 6 are thoroughly methylated by METHYLTRASFERASE1, that CpG methylation levels are inversely correlated with ETT/ARF3 transcript levels and that methylation levels at three out of the six CpG dinucleotides are decreased in as2-1. All these imply that AS2 is involved in epigenetic repression of ETT/ARF3 by gene body DNA methylation...
July 1, 2018: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29298893/allosteric-control-of-human-cystathionine-%C3%AE-synthase-activity-by-a-redox-active-disulfide-bond
#9
Weining Niu, Jun Wang, Jing Qian, Mengying Wang, Ping Wu, Fei Chen, Shasha Yan
Cystathionine β-synthase (CBS) is the central enzyme in the trans-sulfuration pathway that converts homocysteine to cysteine. It is also one of the three major enzymes involved in the biogenesis of H2 S. CBS is a complex protein with a modular three-domain architecture, the central domain of which contains a272 C XX C275 motif whose function has yet to be determined. In the present study, we demonstrated that the C XX C motif exists in oxidized and reduced states in the recombinant enzyme by mass spectroscopic analysis and a thiol labeling assay...
February 16, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29276034/dna-sequence-recognition-of-human-cxxc-domains-and-their-structural-determinants
#10
Chao Xu, Ke Liu, Ming Lei, Ally Yang, Yanjun Li, Timothy R Hughes, Jinrong Min
The CXXC domain, first identified as the reader of unmodified CpG dinucleotide, plays important roles in epigenetic regulation by targeting various activities to CpG islands. Here we systematically measured and compared the DNA-binding selectivities of all known human CXXC domains by different binding assays, and complemented the existing function-based classification of human CXXC domains with a classification based on their DNA selectivities. Through a series of crystal structures of CXXC domains with DNA ligands, we unravel the molecular mechanisms of how these CXXC domains, including single CXXC domains and tandem CXXC-PHD domains, recognize distinct DNA ligands, which further supports our classification of human CXXC domains and also provides insights into selective recruitment of chromatin modifiers to their respective targets via CXXC domains recognizing different genomic DNA sequences...
January 2, 2018: Structure
https://www.readbyqxmd.com/read/29203834/molecular-and-cellular-issues-of-kmt2a-variants-involved-in-wiedemann-steiner-syndrome
#11
Nicolas Lebrun, Irina Giurgea, Alice Goldenberg, Anne Dieux, Alexandra Afenjar, Jamal Ghoumid, Bertrand Diebold, Léo Mietton, Audrey Briand-Suleau, Pierre Billuart, Thierry Bienvenu
Variants in KMT2A, encoding the histone methyltransferase KMT2A, are a growing cause of intellectual disability (ID). Up to now, the majority of KMT2A variants are non-sense and frameshift variants causing a typical form of Wiedemann-Steiner syndrome. We studied KMT2A gene in a cohort of 200 patients with unexplained syndromic and non-syndromic ID and identified four novel variants, one splice and three missense variants, possibly deleterious. We used primary cells from the patients and molecular approaches to determine the deleterious effects of those variants on KMT2A expression and function...
January 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29036306/cxxc5-suppresses-hepatocellular-carcinoma-by-promoting-tgf-%C3%AE-induced-cell-cycle-arrest-and-apoptosis
#12
Xiaohua Yan, Jingyi Wu, Quanlong Jiang, Hao Cheng, Jing-Dong J Han, Ye-Guang Chen
Evading TGF-β-mediated growth inhibition is often associated with tumorigenesis in liver, including hepatocellular carcinoma (HCC). To better understand the functions and the underlying molecular mechanisms of TGF-β in HCC initiation and progression, we carried out transcriptome sequencing (RNA-Seq) to identify the target genes of TGF-β. CXXC5, a member of the CXXC-type zinc finger domain-containing protein family, was identified as a novel TGF-β target gene in Hep3B HCC cells. Knockdown of CXXC5 attenuated the expression of a substantial portion of TGF-β target genes and ameliorated TGF-β-induced growth inhibition or apoptosis of Hep3B cells, suggesting that CXXC5 is required for TGF-β-mediated inhibition of HCC progression...
February 1, 2018: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/29029740/a-quantitative-homogeneous-assay-for-global-dna-methylation-levels-using-cpg-binding-domain-and-methyl-cpg-binding-domain-fused-luciferase
#13
Wataru Yoshida, Yuji Baba, Kyoko Banzawa, Isao Karube
Global DNA methylation levels have been considered as biomarkers for cancer diagnostics because transposable elements that constitute approximately 45% of the human genome are hypomethylated in cancer cells. We have previously reported a homogeneous assay for measuring methylated CpG content of genomic DNA based on bioluminescence resonance energy transfer (BRET) using methyl-CpG-binding domain (MBD)-fused luciferase (MBD-luciferase). In this study, a homogeneous assay for measuring unmethylated CpG content of genomic DNA in the same platform was developed using CXXC domain-fused luciferase (CXXC-luciferase) that specifically recognizes unmethylated CpG...
October 16, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28899103/drfrne-represents-a-hitherto-unknown-class-of-eubacterial-cytoplasmic-disulfide-oxido-reductases
#14
Subhash C Bihani, Lata Panicker, Yogendra S Rajpurohit, Hari S Misra, Vinay Kumar
AIMS: Living cells employ thioredoxin and glutaredoxin disulfide oxido-reductases to protect thiol groups in intracellular proteins. FrnE protein of Deinococcus radiodurans (drFrnE) is a disulfide oxido-reductase that is induced in response to Cd2+ exposure and is involved in cadmium and radiation tolerance. The aim of this study is to probe structure, function, and cellular localization of FrnE class of proteins. RESULTS: Here, we show drFrnE as a novel cytoplasmic oxido-reductase that could be functional in eubacteria under conditions where thioredoxin/glutaredoxin systems are inhibited or absent...
February 1, 2018: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28855337/an-epigenetic-switch-repressing-tet1-in-gonadotropes-activates-the-reproductive-axis
#15
Yahav Yosefzon, Cfir David, Anna Tsukerman, Lilach Pnueli, Sen Qiao, Ulrich Boehm, Philippa Melamed
The TET enzymes catalyze conversion of 5-methyl cytosine (5mC) to 5-hydroxymethyl cytosine (5hmC) and play important roles during development. TET1 has been particularly well-studied in pluripotent stem cells, but Tet1 -KO mice are viable, and the most marked defect is abnormal ovarian follicle development, resulting in impaired fertility. We hypothesized that TET1 might play a role in the central control of reproduction by regulating expression of the gonadotropin hormones, which are responsible for follicle development and maturation and ovarian function...
September 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28532685/nitroxide-4-hydroxy-2-2-6-6-tetramethylpiperidine-1-oxyl-tempol-inhibits-the-reductase-activity-of-protein-disulfide-isomerase-via-covalent-binding-to-the-cys400-residue-on-cxxc-redox-motif-at-the-a-active-site
#16
Gérsika Bitencourt Santos, Lucia Gonzalez-Perilli, Mauricio Mastrogiovanni, Adrián Aicardo, Cláudio Daniel Cerdeira, Andrés Trostchansky, Maísa Ribeiro Pereira Lima Brigagão
BACKGROUND AND AIM: Oxidative stress arising from inflammatory processes is a serious cause of cell and tissue damage. Tempol is an efficient antioxidant with superoxide dismutase-like activity. The purpose of this paper is to address the inhibition of protein disulfide isomerase (PDI), an essential redox chaperone whose active sites contain the Cys-Gly-His-Cys (CXXC) motif, by the nitroxide Tempol. RESULTS: In the presence of Tempol (5-120 μM), the reductase activity of PDI was reversibly affected both in vitro and in activated mice neutrophils, with an IC50 of 22...
June 25, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/28531272/a-novel-isoform-of-tet1-that-lacks-a-cxxc-domain-is-overexpressed-in-cancer
#17
Charly R Good, Jozef Madzo, Bela Patel, Shinji Maegawa, Nora Engel, Jaroslav Jelinek, Jean-Pierre J Issa
TET1 oxidizes methylated cytosine into 5-hydroxymethylcytosine (5hmC), resulting in regulation of DNA methylation and gene expression. Full length TET1 (TET1FL) has a CXXC domain that binds to unmethylated CpG islands (CGIs). This CXXC domain allows TET1 to protect CGIs from aberrant methylation, but it also limits its ability to regulate genes outside of CGIs. Here, we report a novel isoform of TET1 (TET1ALT) that has a unique transcription start site from an alternate promoter in intron 2, yielding a protein with a unique translation start site...
August 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28453857/fbxl19-recruitment-to-cpg-islands-is-required-for-rnf20-mediated-h2b-mono-ubiquitination
#18
Bum-Kyu Lee, Jiwoon Lee, Wenwen Shen, Catherine Rhee, Haewon Chung, Jonghwan Kim
Histone H2B lysine 120 mono-ubiquitination (H2Bub1) catalyzed by Rnf20 has been implicated in normal differentiation of embryonic stem (ES) and adult stem cells. However, it remains unknown how Rnf20 is recruited to its specific target chromosomal loci for the establishment of H2Bub1. Here, we reveal that Fbxl19, a CxxC domain-containing protein, promotes H2Bub1 at the promoters of CpG island-containing genes by interacting with Rnf20. We show that up-regulation of Fbxl19 increases the level of global H2Bub1 in mouse ES cells, while down-regulation of Fbxl19 reduces the level of H2Bub1...
July 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28350064/sf-kdm2a-binds-to-ribosomal-rna-gene-promoter-reduces-h4k20me3-level-and-elevates-ribosomal-rna-transcription-in-breast-cancer-cells
#19
Kengo Okamoto, Yuji Tanaka, Makoto Tsuneoka
Regulation of rRNA transcription is an important factor for control of cell proliferation. We previously found that the JmjC domain-containing demethylase KDM2A reduces H3K36me2 in the rRNA gene promoter and rRNA transcription under starvation, which results in suppression of cell proliferation. The KDM2A gene also produces another protein product, SF-KDM2A, which lacks a JmjC domain and has no demethylase activity. As yet, the function of SF-KDM2A is not clear. Recently, it was reported that KDM2A was frequently amplified and that elevated expression of KDM2A was significantly associated with short survival of breast cancer patients...
March 10, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28212275/identification-and-characterization-of-lipopolysaccharide-induced-tnf%C3%AE-factor-from-blunt-snout-bream-megalobrama-amblycephala
#20
Yina Lv, Xinying Xiang, Yuhong Jiang, Leilei Tang, Yi Zhou, Huan Zhong, Jun Xiao, Jinpeng Yan
Lipopolysaccharide induced TNFα factor (LITAF) is an important transcription factor responsible for regulation of tumor necrosis factor α. In this study, a novel litaf gene (designated as Malitaf) was identified and characterized from blunt snout bream, Megalobrama amblycephala. The full-length cDNA of Malitaf was of 956 bp, encoding a polypeptide of 161 amino acids with high similarity to other known LITAFs. A phylogenetic tree also showed that Malitaf significantly clustered with those of other teleost, indicating that Malitaf was a new member of fish LITAF family...
February 15, 2017: International Journal of Molecular Sciences
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