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Yu Zhao, Miranda C Mudge, Jennifer M Soll, Rachel B Rodrigues, Andrea K Byrum, Elizabeth A Schwarzkopf, Tara R Bradstreet, Steven P Gygi, Brian T Edelson, Nima Mosammaparast
Ubiquitination is a major mechanism that regulates numerous cellular processes, including autophagy, DNA damage signaling, and inflammation. While hundreds of ubiquitin ligases exist to conjugate ubiquitin onto substrates, approximately 100 deubiquitinases are encoded by the human genome. Thus, deubiquitinases are likely regulated by unidentified mechanisms to target distinct substrates and cellular functions. Here, we demonstrate that the deubiquitinase OTUD4, which nominally encodes a K48-specific deubiquitinase, is phosphorylated near its catalytic domain, activating a latent K63-specific deubiquitinase...
February 1, 2018: Molecular Cell
Lucas S Torati, Hervé Migaud, Mary K Doherty, Justyna Siwy, Willian Mullen, Pedro E C Mesquita, Amaya Albalat
Parental investment in Arapaima gigas includes nest building and guarding, followed by a care provision when a cephalic fluid is released from the parents' head to the offspring. This fluid has presumably important functions for the offspring but so far its composition has not been characterised. In this study the proteome and peptidome of the cephalic secretion was studied in parental and non-parental fish using capillary electrophoresis coupled to mass spectrometry (CE-MS) and GeLC-MS/MS analyses. Multiple comparisons revealed 28 peptides were significantly different between males and parental males (PC-males), 126 between females and parental females (PC-females), 51 between males and females and 9 between PC-males and PC-females...
2017: PloS One
Zhe Xue, Jia-Xu Chen, Yue Zhao, Barbara Medvar, Mark A Knepper
A major challenge in physiology is to exploit the many large-scale data sets available from "-omic" studies to seek answers to key physiological questions. In previous studies, Bayes' theorem has been used for this purpose. This approach requires a means to map continuously distributed experimental data to probabilities (likelihood values) to derive posterior probabilities from the combination of prior probabilities and new data. Here, we introduce the use of minimum Bayes' factors for this purpose and illustrate the approach by addressing a physiological question, "Which deubiquitylating enzymes (DUBs) encoded by mammalian genomes are most likely to regulate plasma membrane transport processes in renal cortical collecting duct principal cells?" To do this, we have created a comprehensive online database of 110 DUBs present in the mammalian genome (https://hpcwebapps...
March 1, 2017: Physiological Genomics
Marcell Louis, Kay Hofmann, Meike Broemer
Understanding function and specificity of de-ubiquitylating enzymes (DUBs) is a major goal of current research, since DUBs are key regulators of ubiquitylation events and have been shown to be mutated in human diseases. Most DUBs are cysteine proteases, relying on a catalytic triad of cysteine, histidine and aspartate to cleave the isopeptide bond between two ubiquitin units in a poly-ubiquitin chain. We have discovered that the two Drosophila melanogaster homologues of human OTUD4, CG3251 and Otu, contain a serine instead of a cysteine in the catalytic OTU (ovarian tumor) domain...
2015: PloS One
Yu Zhao, Mona C Majid, Jennifer M Soll, Joshua R Brickner, Sebastian Dango, Nima Mosammaparast
Repair of DNA alkylation damage is critical for genomic stability and involves multiple conserved enzymatic pathways. Alkylation damage resistance, which is critical in cancer chemotherapy, depends on the overexpression of alkylation repair proteins. However, the mechanisms responsible for this upregulation are unknown. Here, we show that an OTU domain deubiquitinase, OTUD4, is a positive regulator of ALKBH2 and ALKBH3, two DNA demethylases critical for alkylation repair. Remarkably, we find that OTUD4 catalytic activity is completely dispensable for this function...
June 12, 2015: EMBO Journal
Ketil Heimdal, Monica Sanchez-Guixé, Ingvild Aukrust, Jens Bollerslev, Ove Bruland, Greg Eigner Jablonski, Anne Kjersti Erichsen, Einar Gude, Jeanette A Koht, Sigrid Erdal, Torunn Fiskerstrand, Bjørn Ivar Haukanes, Helge Boman, Lise Bjørkhaug, Chantal M E Tallaksen, Per M Knappskog, Stefan Johansson
BACKGROUND: A subset of hereditary cerebellar ataxias is inherited as autosomal recessive traits (ARCAs). Classification of recessive ataxias due to phenotypic differences in the cerebellum and cerebellar structures is constantly evolving due to new identified disease genes. Recently, reports have linked mutations in genes involved in ubiquitination (RNF216, OTUD4, STUB1) to ARCA with hypogonadism. METHODS AND RESULTS: With a combination of homozygozity mapping and exome sequencing, we identified three mutations in STUB1 in two families with ARCA and cognitive impairment; a homozygous missense variant (c...
September 26, 2014: Orphanet Journal of Rare Diseases
Angeliki-Maria Vlaikou, Emmanouil Manolakos, Dimitrios Noutsopoulos, Georgios Markopoulos, Thomas Liehr, Annalisa Vetro, Monika Ziegler, Anja Weise, Katharina Kreskowski, Ioannis Papoulidis, Loretta Thomaidis, Maria Syrrou
The 4q deletion syndrome phenotype consists of growth failure and developmental delay, minor craniofacial dysmorphism, digital anomalies, and cardiac and skeletal defects. We have identified an inversion (inv(1)(q25.2q31.1)) and an interstitial deletion in a boy with developmental delay using array-comparative genomic hybridization. This de novo deletion is located at 4q31.21q31.22 (145,963,820- 147,044,764), its size is 0.9-1.1 Mb, and it contains 7 genes (ABCE1, OTUD4, SMAD1, MMAA, C4orf51, ZNF827, and ANAPC10) as well as 5 retrotransposon-derived pseudogenes...
2014: Cytogenetic and Genome Research
Abigail Lubin, Ling Zhang, Hua Chen, Victoria M White, Feng Gong
Global genome nucleotide excision repair (GG-NER) is responsible for identifying and removing bulky adducts from non-transcribed DNA that result from damaging agents such as UV radiation and cisplatin. Xeroderma pigmentosum complementation group C (XPC) is one of the essential damage recognition proteins of the GG-NER pathway and its dysfunction results in xeroderma pigmentosum (XP), a disorder involving photosensitivity and a predisposition to cancer. To better understand the identification of DNA damage by XPC in the context of chromatin and the role of XPC in the pathogenesis of XP, we characterized the interactome of XPC using a high throughput yeast two-hybrid screening...
December 23, 2013: International Journal of Molecular Sciences
Chang-He Shi, Jonathan C Schisler, Carrie E Rubel, Song Tan, Bo Song, Holly McDonough, Lei Xu, Andrea L Portbury, Cheng-Yuan Mao, Cadence True, Rui-Hao Wang, Qing-Zhi Wang, Shi-Lei Sun, Stephanie B Seminara, Cam Patterson, Yu-Ming Xu
Gordon Holmes syndrome (GHS) is a rare Mendelian neurodegenerative disorder characterized by ataxia and hypogonadism. Recently, it was suggested that disordered ubiquitination underlies GHS though the discovery of exome mutations in the E3 ligase RNF216 and deubiquitinase OTUD4. We performed exome sequencing in a family with two of three siblings afflicted with ataxia and hypogonadism and identified a homozygous mutation in STUB1 (NM_005861) c.737C→T, p.Thr246Met, a gene that encodes the protein CHIP (C-terminus of HSC70-interacting protein)...
February 15, 2014: Human Molecular Genetics
William Ka Fai Tse, Yun-Jin Jiang, Chris Kong Chu Wong
BACKGROUND: Osmotic stress transcription factor 1/transforming growth factor-β-stimulated clone 22 domain 3 (Ostf1/Tsc22d3) is a transcription factor that plays an osmoregulatory role in euryhaline fishes. Its mRNA and protein levels are up-regulated under hyperosmotic stress. However, its osmoregulatory and developmental functions have not been studied in any stenohaline freshwater fishes. Zebrafish is an excellent model to perform such study to unfold the functional role of Tsc22d3...
October 2013: Biochimica et Biophysica Acta
David H Margolin, Maria Kousi, Yee-Ming Chan, Elaine T Lim, Jeremy D Schmahmann, Marios Hadjivassiliou, Janet E Hall, Ibrahim Adam, Andrew Dwyer, Lacey Plummer, Stephanie V Aldrin, Julia O'Rourke, Andrew Kirby, Kasper Lage, Aubrey Milunsky, Jeff M Milunsky, Jennifer Chan, E Tessa Hedley-Whyte, Mark J Daly, Nicholas Katsanis, Stephanie B Seminara
BACKGROUND: The combination of ataxia and hypogonadism was first described more than a century ago, but its genetic basis has remained elusive. METHODS: We performed whole-exome sequencing in a patient with ataxia and hypogonadotropic hypogonadism, followed by targeted sequencing of candidate genes in similarly affected patients. Neurologic and reproductive endocrine phenotypes were characterized in detail. The effects of sequence variants and the presence of an epistatic interaction were tested in a zebrafish model...
May 23, 2013: New England Journal of Medicine
William K F Tse, Birgit Eisenhaber, Steven H K Ho, Qimei Ng, Frank Eisenhaber, Yun-Jin Jiang
BACKGROUND: Deconjugation of ubiquitin and/or ubiquitin-like modified protein substrates is essential to modulate protein-protein interactions and, thus, signaling processes in cells. Although deubiquitylating (deubiquitinating) enzymes (DUBs) play a key role in this process, however, their function and regulation remain insufficiently understood. The "loss-of-function" phenotype studies can provide important information to elucidate the gene function, and zebrafish is an excellent model for this goal...
2009: BMC Genomics
D C Crawford, N Zheng, E C Speelmon, I Stanaway, M J Rieder, D A Nickerson, M J McElrath, J Lingappa
Signatures of natural selection occur throughout the human genome and can be detected at the sequence level. We have re-sequenced ABCE1, a host candidate gene essential for HIV-1 capsid assembly, in European- (n=23) and African-descent (Yoruban; n=24) reference populations for genetic variation discovery. We identified an excess of rare genetic variation in Yoruban samples, and the resulting Tajima's D was low (-2.27). The trend of excess rare variation persisted in flanking candidate genes ANAPC10 and OTUD4, suggesting that this pattern of positive selection can be detected across the 184...
December 2009: Genes and Immunity
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