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https://www.readbyqxmd.com/read/28134789/mrpl10-and-tbp-are-suitable-reference-genes-for-peripheral-nerve-crush-injury
#1
Yaxian Wang, Qianqian Shan, Yali Meng, Jiacheng Pan, Sheng Yi
Peripheral nerve injury triggers the dysregulation of a large number of genes at multiple sites, including neurons, peripheral nerve stump, and the target organ. Housekeeping genes were frequently used as reference genes to normalize the expression values of target genes. Suitable selection of housekeeping genes that are stably expressed after nerve injury minimizes bias elicited by reference genes and thus helps to better and more sensitively reflect gene expression changes. However, many housekeeping genes have been used as reference genes without testing the expression patterns of themselves...
January 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28115426/p97-negatively-regulates-nrf2-by-extracting-ubiquitylated-nrf2-from-the-keap1-cul3-e3-complex
#2
Shasha Tao, Pengfei Liu, Gang Luo, Montserrat Rojo de la Vega, Heping Chen, Tongde Wu, Joseph Tillotson, Eli Chapman, Donna D Zhang
Activation of the stress responsive transcription factor NRF2 is the major line of defense to combat oxidative or electrophilic insults. Under basal conditions, NRF2 is continuously ubiquitylated by the KEAP1-CUL3-RBX1 E3 ubiquitin ligase complex and targeted to the proteasome for degradation (the canonical mechanism). However, the path from the CUL3 complex to ultimate proteasomal degradation had been previously unknown. p97 is an ubiquitin-targeted ATP-dependent segregase that extracts ubiquitylated client proteins from membranes, protein complexes, or chromatin and has an essential role in autophagy and the ubiquitin proteasome system (UPS)...
January 23, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27913640/the-drosophila-hox-gene-ultrabithorax-acts-both-in-muscles-and-motoneurons-to-orchestrate-formation-of-specific-neuromuscular-connections
#3
Christian Hessinger, Gerhard M Technau, Ana Rogulja-Ortmann
Hox genes are known to specify motoneuron pools in the developing vertebrate spinal cord and to control motoneuronal targeting in several species. However, the mechanisms controlling axial diversification of muscle innervation patterns are still largely unknown. We present data showing that the Drosophila Hox gene Ultrabithorax (Ubx) acts in the late embryo to establish target specificity of ventrally projecting RP motoneurons. In abdominal segments A2 to A7, RP motoneurons innervate the ventro-lateral muscles VL1-4, with VL1 and VL2 being innervated in a Wnt4-dependent manner...
December 2, 2016: Development
https://www.readbyqxmd.com/read/27913212/vcp-cooperates-with-ubxd1-to-degrade-mitochondrial-outer-membrane-protein-mcl1-in-model-of-huntington-s-disease
#4
Xing Guo, Xin Qi
Proteasome-dependent turnover of mitochondrial outer membrane (OMM)-associated proteins is one of the mechanisms for maintaining proper mitochondrial quality and function. However, the underlying pathways and their implications in human disease are poorly understood. Huntington's disease (HD) is a fatal, inherited neurodegenerative disorder caused by expanded CAG repeats in the N terminal of the huntingtin gene (mutant Huntingtin, mtHtt). In this study, we show an extensive degradation of the OMM protein MCL1 (Myeloid cell leukemia sequence 1) in both HD mouse striatal cells and HD patient fibroblasts...
February 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27848019/non-specificity-of-transcription-factor-function-in-drosophila-melanogaster
#5
Anthony Percival-Smith
A major problem in developmental genetics is how HOX transcription factors, like Proboscipedia (PB) and Ultrabithorax (UBX), regulate distinct programs of gene expression to result in a proboscis versus a haltere, respectively, when the DNA-binding homeodomain (HD) of HOX transcription factors recognizes similar DNA-binding sequences. Indeed, the lack of DNA-binding specificity is a problem for all transcription factors (TFs), as the DNA-binding domains generally recognize small targets of five to six bases in length...
January 2017: Development Genes and Evolution
https://www.readbyqxmd.com/read/27813696/chromatin-changes-in-smarcal1-deficiency-a-hypothesis-for-the-gene-expression-alterations-of-schimke-immuno-osseous-dysplasia
#6
Marie Morimoto, Kunho Choi, Cornelius F Boerkoel, Kyoung Sang Cho
Mutations in SMARCAL1, which encodes a DNA annealing helicase with roles in DNA replication fork restart, DNA repair, and gene expression modulation, cause Schimke immuno-osseous dysplasia (SIOD), an autosomal recessive disease characterized by skeletal dysplasia, renal disease, T-cell immunodeficiency, and arteriosclerosis. The clinical features of SIOD arise from pathological changes in gene expression; however, the underlying mechanism for these gene expression alterations remains unclear. We hypothesized that changes of the epigenome alter gene expression in SIOD...
November 2016: Nucleus
https://www.readbyqxmd.com/read/27785701/the-opposite-role-of-two-uba-ubx-containing-proteins-p47-and-saks1-in-the-degradation-of-a-single-erad-substrate-%C3%AE-tcr
#7
Eun Sil Park, Yung Joon Yoo, Muthukumar Elangovan
The UBA-UBX domain-containing proteins can interact with ubiquitinated substrates and p97 during endoplasmic reticulum-associated degradation (ERAD). Here, we found that the expressions of all UBA-UBX genes p47, SAKS1, UBXD8, FAF1, and UBXD7 were elevated upon ER stress, albeit with different levels. Of which p47, SAKS1, and UBXD8 are 'immediate' respondents whereas FAF1 and UBXD7 were 'late' respondents to ER stress. Interestingly, the expression of specific UBA-UBX genes were altered in cells stably expressing three different ERAD substrates such as α-TCR, α1-antitrypsin, and δCD3...
January 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/27762274/quantitative-interaction-mapping-reveals-an-extended-ubx-domain-in-aspl-that-disrupts-functional-p97-hexamers
#8
Anup Arumughan, Yvette Roske, Carolin Barth, Laura Lleras Forero, Kenny Bravo-Rodriguez, Alexandra Redel, Simona Kostova, Erik McShane, Robert Opitz, Katja Faelber, Kirstin Rau, Thorsten Mielke, Oliver Daumke, Matthias Selbach, Elsa Sanchez-Garcia, Oliver Rocks, Daniela Panáková, Udo Heinemann, Erich E Wanker
Interaction mapping is a powerful strategy to elucidate the biological function of protein assemblies and their regulators. Here, we report the generation of a quantitative interaction network, directly linking 14 human proteins to the AAA+ ATPase p97, an essential hexameric protein with multiple cellular functions. We show that the high-affinity interacting protein ASPL efficiently promotes p97 hexamer disassembly, resulting in the formation of stable p97:ASPL heterotetramers. High-resolution structural and biochemical studies indicate that an extended UBX domain (eUBX) in ASPL is critical for p97 hexamer disassembly and facilitates the assembly of p97:ASPL heterotetramers...
October 20, 2016: Nature Communications
https://www.readbyqxmd.com/read/27754413/ubxd-proteins-a-family-of-proteins-with-diverse-functions-in-cancer
#9
REVIEW
Khosrow Rezvani
The UBXD family is a diverse group of UBX (ubiquitin-regulatory X) domain-containing proteins in mammalian cells. Members of this family contain a UBX domain typically located at the carboxyl-terminal of the protein. In contrast to the UBX domain shared by all members of UBXD family, the amino-terminal domains are diverse and appear to carry out different roles in a subcellular localization-dependent manner. UBXD proteins are principally associated with the endoplasmic reticulum (ER), where they positively or negatively regulate the ER-associated degradation machinery (ERAD)...
October 14, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27715013/functionalization-of-ultrabithorax-materials-with-vascular-endothelial-growth-factor-enhances-angiogenic-activity
#10
David W Howell, Camille L Duran, Shang-Pu Tsai, Sarah E Bondos, Kayla J Bayless
Successful design of tissue engineering scaffolds must include the ability to stimulate vascular development by incorporating angiogenic growth factors. Current approaches can allow diffusion of growth factors, incorporate active factors randomly, or can leave residual toxins. We addressed these problems by genetically fusing the gene encoding Vascular Endothelial Growth Factor (VEGF) with the Ultrabithorax (Ubx) gene to produce fusion proteins capable of self-assembly into materials. We demonstrate that VEGF-Ubx materials enhance human endothelial cell migration, prolong cell survival, and dose-dependently activate the VEGF signaling pathway...
November 14, 2016: Biomacromolecules
https://www.readbyqxmd.com/read/27588071/co-expression-network-analysis-of-down-s-syndrome-based-on-microarray-data
#11
Jianping Zhao, Zhengguo Zhang, Shumin Ren, Yanan Zong, Xiangdong Kong
Down's syndrome (DS) is a type of chromosome disease. The present study aimed to explore the underlying molecular mechanisms of DS. GSE5390 microarray data downloaded from the gene expression omnibus database was used to identify differentially expressed genes (DEGs) in DS. Pathway enrichment analysis of the DEGs was performed, followed by co-expression network construction. Significant differential modules were mined by mutual information, followed by functional analysis. The accuracy of sample classification for the significant differential modules of DEGs was evaluated by leave-one-out cross-validation...
September 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/27575958/genome-wide-ultrabithorax-binding-analysis-reveals-highly-targeted-genomic-loci-at-developmental-regulators-and-a-potential-connection-to-polycomb-mediated-regulation
#12
Daria Shlyueva, Antonio C A Meireles-Filho, Michaela Pagani, Alexander Stark
Hox homeodomain transcription factors are key regulators of animal development. They specify the identity of segments along the anterior-posterior body axis in metazoans by controlling the expression of diverse downstream targets, including transcription factors and signaling pathway components. The Drosophila melanogaster Hox factor Ultrabithorax (Ubx) directs the development of thoracic and abdominal segments and appendages, and loss of Ubx function can lead for example to the transformation of third thoracic segment appendages (e...
2016: PloS One
https://www.readbyqxmd.com/read/27570230/ubx-dynamically-regulates-dpp-signaling-by-repressing-dad-expression-during-copper-cell-regeneration-in-the-adult-drosophila-midgut
#13
Hongjie Li, Yanyan Qi, Heinrich Jasper
The gastrointestinal (GI) tract of metazoans is lined by a series of regionally distinct epithelia. To maintain structure and function of the GI tract, regionally diversified differentiation of somatic stem cell (SC) lineages is critical. The adult Drosophila midgut provides an accessible model to study SC regulation and specification in a regionally defined manner. SCs of the posterior midgut (PM) have been studied extensively, but the control of SCs in the middle midgut (MM) is less well understood. The MM contains a stomach-like copper cell region (CCR) that is regenerated by gastric stem cells (GSSCs) and contains acid-secreting copper cells (CCs)...
November 15, 2016: Developmental Biology
https://www.readbyqxmd.com/read/27462546/urinary-bladder-xanthoma-is-immunohistochemistry-necessary
#14
M Raghavendran, A Venugopal, Vinay N Kaushik
Urinary Bladder Xanthomas (UBX) are non-neoplastic reactive tumor like process. Isolated UBX is rare with only around 15 cases reported (Yu, Patel, & Bonert, 2015). UBX are reported in older patients who present with non specific symptoms like UTI or hematuria. Patients often have associated lipid anomalies. UBX have been vaguely described as yellowish white plaques or patches. Also, recent reports have stressed on the role of Immunohistochemistry in the diagnosis (Al-Daraji, Varghese, & Husain, 2007; Vimal, Masih, Manipadam, & Chacko, 2012)...
September 2016: Urology Case Reports
https://www.readbyqxmd.com/read/27407164/structural-insights-into-the-interaction-of-p97-n-terminus-domain-and-vbm-in-rhomboid-protease-rhbdl4
#15
Jia Jia Lim, Youngjin Lee, Tue Tu Ly, Jung Youn Kang, Jung-Gyu Lee, Jun Yop An, Hyung-Seop Youn, Kyoung Ryoung Park, Tae Gyun Kim, Jin Kuk Yang, Youngsoo Jun, Soo Hyun Eom
RHBDL4 is an active rhomboid that specifically recognizes and cleaves atypical, positively charged transmembrane endoplasmic reticulum-associated degradation (ERAD) substrates. Interaction of valosin-containing protein (p97/VCP) and RHBDL4 is crucial to retrotranslocate polyubiquitinated substrates for ERAD pathway. Here, we report the first complex structure of VCP-binding motif (VBM) with p97 N-terminal domain (p97N) at 1.88 Å resolution. Consistent with p97 adaptor proteins including p47-ubiquitin regulatory X (UBX), gp78-VCP-interacting motif (VIM), OTU1-UBX-like element, and FAF1-UBX, RHBDL4 VBM also binds at the interface between the two lobes of p97N...
September 15, 2016: Biochemical Journal
https://www.readbyqxmd.com/read/27296678/a-comparative-genomic-analysis-of-targets-of-hox-protein-ultrabithorax-amongst-distant-insect-species
#16
Naveen Prasad, Shreeharsha Tarikere, Dhanashree Khanale, Farhat Habib, L S Shashidhara
In the fruitfly Drosophila melanogaster, the differential development of wing and haltere is dependent on the function of the Hox protein Ultrabithorax (Ubx). Here we compare Ubx-mediated regulation of wing patterning genes between the honeybee, Apis mellifera, the silkmoth, Bombyx mori and Drosophila. Orthologues of Ubx are expressed in the third thoracic segment of Apis and Bombyx, although they make functional hindwings. When over-expressed in transgenic Drosophila, Ubx derived from Apis or Bombyx could suppress wing development, suggesting evolutionary changes at the level of co-factors and/or targets of Ubx...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27132113/mutant-p97-exhibits-species-specific-changes-of-its-atpase-activity-and-compromises-the-ubxd9-mediated-monomerisation-of-p97-hexamers
#17
Ramesh Rijal, Khalid Arhzaouy, Karl-Heinz Strucksberg, Megan Cross, Andreas Hofmann, Rolf Schröder, Christoph S Clemen, Ludwig Eichinger
p97 (VCP) is a homo-hexameric triple-A ATPase that exerts a plethora of cellular processes. Heterozygous missense mutations of p97 cause at least five human neurodegenerative disorders. However, the specific molecular consequences of p97 mutations are hitherto widely unknown. Our in silico structural models of human and Dictyostelium p97 showed that the disease-causing human R93C, R155H, and R155C as well as Dictyostelium R154C, E219K, R154C/E219K p97 mutations constitute variations in surface-exposed locations...
June 2016: European Journal of Cell Biology
https://www.readbyqxmd.com/read/26833546/identification-of-hox-genes-and-rearrangements-within-the-single-homeobox-hox-cluster-192-8%C3%A2-kb-of-the-cyclopoid-copepod-paracyclopina-nana
#18
Hui-Su Kim, Bo-Mi Kim, Bo-Young Lee, Sami Souissi, Heum Gi Park, Jae-Seong Lee
We report the first identification of the entire complement of the eight typical homeobox (hox) genes (lab, pb, Dfd, scr, antp, ubx, Abd-A, and Abd-B) and the ftz gene in a 192.8 kb region in the cyclopoid copepod Paracyclopina nana. A Hox3 gene ortholog was not present in the P. nana hox gene cluster, while the P. nana Dfd gene was transcribed in the opposite direction to the Daphnia pulex Dfd gene, but in the same direction as the Dfd genes of the fruit fly Drosophila melanogaster and red flour beetle Tribolium castaneum...
March 2016: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/26715665/distinct-roles-of-chromatin-insulator-proteins-in-control-of-the-drosophila-bithorax-complex
#19
Mikhail Savitsky, Maria Kim, Oksana Kravchuk, Yuri B Schwartz
Chromatin insulators are remarkable regulatory elements that can bring distant genomic sites together and block unscheduled enhancer-promoter communications. Insulators act via associated insulator proteins of two classes: sequence-specific DNA binding factors and "bridging" proteins. The latter are required to mediate interactions between distant insulator elements. Chromatin insulators are critical for correct expression of complex loci; however, their mode of action is poorly understood. Here, we use the Drosophila bithorax complex as a model to investigate the roles of the bridging proteins Cp190 and Mod(mdg4)...
February 2016: Genetics
https://www.readbyqxmd.com/read/26712034/protein-protein-interactions-indicate-composition-of-a-480-kda-selma-complex-in-the-second-outermost-membrane-of-diatom-complex-plastids
#20
Julia B Lau, Simone Stork, Daniel Moog, Julian Schulz, Uwe G Maier
Most secondary plastids of red algal origin are surrounded by four membranes and nucleus-encoded plastid proteins have to traverse these barriers. Translocation across the second outermost plastid membrane, the periplastidal membrane (PPM), is facilitated by a ERAD-(ER-associated degradation) derived machinery termed SELMA (symbiont-specific ERAD-like machinery). In the last years, important subunits of this translocator have been identified, which clearly imply compositional similarities between SELMA and ERAD...
April 2016: Molecular Microbiology
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