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https://www.readbyqxmd.com/read/28807601/ubx-domain-containing-proteins-are-involved-in-lipid-homeostasis-and-stress-responses-in-pichia-pastoris
#1
Meng Zhang, Qilin Yu, Zhe Liu, Chen Liang, Biao Zhang, Mingchun Li
Ubiquitin regulatory X (UBX) domain-containing proteins constitute a family of proteins and are substrate adaptors of AAA ATPase Cdc48. UBX proteins can bind to the N-terminal region of Cdc48 to perform endoplasmic reticulum associated protein degradation (ERAD). In this study, we identified two UBX domain-containing proteins, Ubx1 and Ubx2, in Pichia pastoris and found that the two proteins could recover the growth defect of Saccharomyces cerevisiae in ubx2Δ. Our results revealed that Ubx1 and Ubx2 play critical roles in synthesis of unsaturated fatty acids by affecting Spt23...
August 11, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28721464/unexpected-ubx-expression-in-the-maxilliped-of-the-mystacocarid-crustacean-derocheilocharis-remanei-evidence-for-a-different-way-of-making-a-maxilliped
#2
Martin Fritsch, Stefan Richter
In terms of morphology, crustacean maxillipeds are hybrid appendages. They arise in anterior thoracic segments and display characteristics of both locomotory (thoracic) and feeding (gnathal) appendages. Maxillipeds are functionally integrated with the anterior gnathal appendages. Hox gene expression patterns and immunolabeling with the FP6.87 antibody, which detects conserved epitopes of UBX and ABD-A proteins, reveal that maxillipeds are consistently associated with a shift in the expression of the homeotic gene Ubx...
July 2017: Development Genes and Evolution
https://www.readbyqxmd.com/read/28642242/specific-expression-and-function-of-the-six3-optix-in-drosophila-serially-homologous-organs
#3
Amer Al Khatib, Natalia Siomava, Antonella Iannini, Nico Posnien, Fernando Casares
Organ size and pattern results from the integration of two positional information systems. One global information system, encoded by the Hox genes, links organ type with position along the main body axis. Within specific organs, local information is conveyed by signaling molecules that regulate organ growth and pattern. The mesothoracic (T2) wing and the metathoracic (T3) haltere of Drosophila represent a paradigmatic example of this coordination. The Hox gene Ultrabithorax (Ubx), expressed in the developing T3, selects haltere identity by, among other processes, modulating the production and signaling efficiency of Dpp, a BMP2-like molecule that acts as a major regulator of size and pattern...
August 15, 2017: Biology Open
https://www.readbyqxmd.com/read/28521947/ultrabithorax-and-the-evolution-of-insect-forewing-hindwing-differentiation
#4
REVIEW
Yoshinori Tomoyasu
Decades have passed since the stunning four-winged phenotype of the Drosophila Ultrabithorax (Ubx) mutant was reported, and accumulating knowledge obtained from studies on Ubx in Drosophila has provided a framework to investigate the role of Ubx during insect wing evolution. With several new insights emerging from recent studies in non-Drosophila insects, along with the outcomes of genomic studies focused on identifying Ubx targets, it appears to be an appropriate time to revisit the Drosophila paradigm regarding insect wing development and evolution...
February 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28421448/the-bxdpre-tre-element-terminates-passing-through-transcription
#5
M M Erokhin, P V Elizar'ev, P G Georgiev, D A Chetverina
The regulation of PRE/TRE activity is required for appropriate tissue and stage-specific gene expression. However, the molecular principles of PRE/TRE activity control remain unknown. Here we show that PRE/TRE element from Ubx regulatory region efficiently terminates passing through transcription.
January 2017: Doklady. Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28368031/housekeeping-in-tephritid-insects-the-best-gene-choice-for-expression-analyses-in-the-medfly-and-the-olive-fly
#6
Efthimia Sagri, Panagiota Koskinioti, Maria-Eleni Gregoriou, Konstantina T Tsoumani, Yiannis C Bassiakos, Kostas D Mathiopoulos
Real-time quantitative-PCR has been a priceless tool for gene expression analyses. The reaction, however, needs proper normalization with the use of housekeeping genes (HKGs), whose expression remains stable throughout the experimental conditions. Often, the combination of several genes is required for accurate normalization. Most importantly, there are no universal HKGs which can be used since their expression varies among different organisms, tissues or experimental conditions. In the present study, nine common HKGs (RPL19, tbp, ubx, GAPDH, α-TUB, β-TUB, 14-3-3zeta, RPE and actin3) are evaluated in thirteen different body parts, developmental stages and reproductive and olfactory tissues of two insects of agricultural importance, the medfly and the olive fly...
April 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28274878/crystal-structures-of-the-ubx-domain-of-human-ubxd7-and-its-complex-with-p97-atpase
#7
Zhi-Hui Li, Yong Wang, Min Xu, Tao Jiang
In humans, UBXD7 (also called UBXN7), an adaptor of p97 ATPase, can participate in the degradation of misfolded or damaged proteins in the p97-mediated ubiquitin proteasome system (UPS). UBXD7 binds to ubiquitinated substrates via its UBA domain and interacts with p97 N-terminal domain through its UBX domain to recruit p97 or the p97 core complex (p97/NPL4/UFD1). Here, we report the crystal structures of the UBX domain of UBXD7 (UBXD7(UBX)) at 2.0 Å resolution and its complex with p97 N-terminal domain (p97(NTD)-UBXD7(UBX) complex) at 2...
April 22, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28134789/mrpl10-and-tbp-are-suitable-reference-genes-for-peripheral-nerve-crush-injury
#8
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
#9
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 is targeted to the proteasome for degradation (the canonical mechanism). However, the path from the CUL3 complex to ultimate proteasomal degradation was previously unknown. p97 is a 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)...
April 15, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27913640/the-drosophila-hox-gene-ultrabithorax-acts-in-both-muscles-and-motoneurons-to-orchestrate-formation-of-specific-neuromuscular-connections
#10
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 ventrolateral muscles VL1-4, with VL1 and VL2 being innervated in a Wnt4-dependent manner...
January 1, 2017: Development
https://www.readbyqxmd.com/read/27913212/vcp-cooperates-with-ubxd1-to-degrade-mitochondrial-outer-membrane-protein-mcl1-in-model-of-huntington-s-disease
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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