Relevant bibliographies by topics / Domain of Unknown Function (DUF) 579

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Academic literature on the topic 'Domain of Unknown Function (DUF) 579'

Author: Grafiati
Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Domain of Unknown Function (DUF) 579"

1

Smith, Peter J., Malcolm A. O’Neill, Jason Backe, William S. York, Maria J. Peña, and Breeanna R. Urbanowicz. "Analytical Techniques for Determining the Role of Domain of Unknown Function 579 Proteins in the Synthesis of O-Methylated Plant Polysaccharides." SLAS TECHNOLOGY: Translating Life Sciences Innovation 25, no. 4 (March 23, 2020): 345–55. http://dx.doi.org/10.1177/2472630320912692.

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Matrix polysaccharides are a diverse group of structurally complex carbohydrates and account for a large portion of the biomass consumed as food or used to produce fuels and materials. Glucuronoxylan and arabinogalactan protein are matrix glycans that have sidechains decorated with 4- O-methyl glucuronosyl residues. Methylation is a key determinant of the physical properties of these wall glycopolymers and consequently affects both their biological function and ability to interact with other wall polymers. Indeed, there is increasing interest in determining the distribution and abundance of methyl-etherified polysaccharides in different plant species, tissues, and developmental stages. There is also a need to understand the mechanisms involved in their biosynthesis. Members of the Domain of Unknown Function (DUF) 579 family have been demonstrated to have a role in the biosynthesis of methyl-etherified glycans. Here we describe methods for the analysis of the 4- O-methyl glucuronic acid moieties that are present in sidechains of arabinogalactan proteins. These methods are then applied toward the analysis of loss-of-function mutants of two DUF579 family members that lack this modification in muro. We also present a procedure to assay DUF579 family members for enzymatic activity in vitro using acceptor oligosaccharides prepared from xylan of loss-of-function mutants. Our approach facilitates the characterization of enzymes that modify glycosyl residues during cell wall synthesis and the structures that they generate.
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Mann, Greg, Jesko Koehnke, Andrew F. Bent, Rachael Graham, Wael Houssen, Marcel Jaspars, Uli Schwarz-Linek, and James H. Naismith. "The structure of the cyanobactin domain of unknown function from PatG in the patellamide gene cluster." Acta Crystallographica Section F Structural Biology Communications 70, no. 12 (November 14, 2014): 1597–603. http://dx.doi.org/10.1107/s2053230x1402425x.

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Patellamides are members of the cyanobactin family of ribosomally synthesized and post-translationally modified cyclic peptide natural products, many of which, including some patellamides, are biologically active. A detailed mechanistic understanding of the biosynthetic pathway would enable the construction of a biotechnological `toolkit' to make novel analogues of patellamides that are not found in nature. All but two of the protein domains involved in patellamide biosynthesis have been characterized. The two domains of unknown function (DUFs) are homologous to each other and are found at the C-termini of the multi-domain proteins PatA and PatG. The domain sequence is found in all cyanobactin-biosynthetic pathways characterized to date, implying a functional role in cyanobactin biosynthesis. Here, the crystal structure of the PatG DUF domain is reported and its binding interactions with plausible substrates are investigated.
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Harada, Kenichi, Eiki Yamashita, Kento Inoue, Koji Yamaguchi, Toshimichi Fujiwara, Atsushi Nakagawa, Tsutomu Kawasaki, and Chojiro Kojima. "Plant-specific DUF1110 protein fromOryza sativa: expression, purification and crystallization." Acta Crystallographica Section F Structural Biology Communications 72, no. 6 (May 23, 2016): 480–84. http://dx.doi.org/10.1107/s2053230x16007573.

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The Os01T0156300 protein fromOryza sativahas been classified into the domain of unknown function (DUF) family DUF1110. DUF1110 family members exist in monocotyledons but not in dicotyledons, and share no sequence identity with proteins for which structures have been reported. In this study, the Os01T0156300 protein was crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 1.84 Å resolution. The crystal belonged to space groupP21, with unit-cell parametersa= 89.9,b= 89.8,c= 107.1 Å, β = 106.6°. The asymmetric unit was estimated to contain 6–11 molecules.
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4

Hwang, Jisun, Bohee Jang, Ayoung Kim, Yejin Lee, Joonha Lee, Chungho Kim, Jinmahn Kim, et al. "Syndecan Transmembrane Domain Specifically Regulates Downstream Signaling Events of the Transmembrane Receptor Cytoplasmic Domain." International Journal of Molecular Sciences 22, no. 15 (July 24, 2021): 7918. http://dx.doi.org/10.3390/ijms22157918.

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Despite the known importance of the transmembrane domain (TMD) of syndecan receptors in cell adhesion and signaling, the molecular basis for syndecan TMD function remains unknown. Using in vivo invertebrate models, we found that mammalian syndecan-2 rescued both the guidance defects in C. elegans hermaphrodite-specific neurons and the impaired development of the midline axons of Drosophila caused by the loss of endogenous syndecan. These compensatory effects, however, were reduced significantly when syndecan-2 dimerization-defective TMD mutants were introduced. To further investigate the role of the TMD, we generated a chimera, 2eTPC, comprising the TMD of syndecan-2 linked to the cytoplasmic domain of platelet-derived growth factor receptor (PDGFR). This chimera exhibited SDS-resistant dimer formation that was lost in the corresponding dimerization-defective syndecan-2 TMD mutant, 2eT(GL)PC. Moreover, 2eTPC specifically enhanced Tyr 579 and Tyr 857 phosphorylation in the PDGFR cytoplasmic domain, while the TMD mutant failed to support such phosphorylation. Finally, 2eTPC, but not 2eT(GL)PC, induced phosphorylation of Src and PI3 kinase (known downstream effectors of Tyr 579 phosphorylation) and promoted Src-mediated migration of NIH3T3 cells. Taken together, these data suggest that the TMD of a syndecan-2 specifically regulates receptor cytoplasmic domain function and subsequent downstream signaling events controlling cell behavior.
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Sun, Chen, Lili Hu, Shousheng Liu, Zhan Gao, and Shicui Zhang. "Functional analysis of domain of unknown function (DUF) 1943, DUF1944 and von Willebrand factor type D domain (VWD) in vitellogenin2 in zebrafish." Developmental & Comparative Immunology 41, no. 4 (December 2013): 469–76. http://dx.doi.org/10.1016/j.dci.2013.07.005.

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6

Pan, Guohui, Zhengren Xu, Zhikai Guo, Hindra, Ming Ma, Dong Yang, Hao Zhou, et al. "Discovery of the leinamycin family of natural products by mining actinobacterial genomes." Proceedings of the National Academy of Sciences 114, no. 52 (December 11, 2017): E11131—E11140. http://dx.doi.org/10.1073/pnas.1716245115.

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Nature’s ability to generate diverse natural products from simple building blocks has inspired combinatorial biosynthesis. The knowledge-based approach to combinatorial biosynthesis has allowed the production of designer analogs by rational metabolic pathway engineering. While successful, structural alterations are limited, with designer analogs often produced in compromised titers. The discovery-based approach to combinatorial biosynthesis complements the knowledge-based approach by exploring the vast combinatorial biosynthesis repertoire found in Nature. Here we showcase the discovery-based approach to combinatorial biosynthesis by targeting the domain of unknown function and cysteine lyase domain (DUF–SH) didomain, specific for sulfur incorporation from the leinamycin (LNM) biosynthetic machinery, to discover the LNM family of natural products. By mining bacterial genomes from public databases and the actinomycetes strain collection at The Scripps Research Institute, we discovered 49 potential producers that could be grouped into 18 distinct clades based on phylogenetic analysis of the DUF–SH didomains. Further analysis of the representative genomes from each of the clades identified 28 lnm-type gene clusters. Structural diversities encoded by the LNM-type biosynthetic machineries were predicted based on bioinformatics and confirmed by in vitro characterization of selected adenylation proteins and isolation and structural elucidation of the guangnanmycins and weishanmycins. These findings demonstrate the power of the discovery-based approach to combinatorial biosynthesis for natural product discovery and structural diversity and highlight Nature’s rich biosynthetic repertoire. Comparative analysis of the LNM-type biosynthetic machineries provides outstanding opportunities to dissect Nature’s biosynthetic strategies and apply these findings to combinatorial biosynthesis for natural product discovery and structural diversity.
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7

Roig, Francisco J., Fernando González-Candelas, and Carmen Amaro. "Domain Organization and Evolution of Multifunctional Autoprocessing Repeats-in-Toxin (MARTX) Toxin inVibrio vulnificus." Applied and Environmental Microbiology 77, no. 2 (November 12, 2010): 657–68. http://dx.doi.org/10.1128/aem.01806-10.

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ABSTRACTThe objective of this study was to analyze multifunctional autoprocessing repeats-in-toxin (MARTX) toxin domain organization within the aquatic speciesVibrio vulnificusas well as to study the evolution of thertxA1gene. The species is subdivided into three biotypes that differ in host range and geographical distribution. We have found three different types (I, II, and III) ofV. vulnificusMARTX (MARTXVv) toxins with common domains (an autocatalytic cysteine protease domain [CPD], an α/β-hydrolase domain, and a domain resembling that of the LifA protein ofEscherichia coliO127:H6 E2348/69 [Efa/LifA]) and specific domains (a Rho-GTPase inactivation domain [RID], a domain of unknown function [DUF],a domain resembling that of thertxAprotein ofPhotorhabdus asymbiotica[rtxAPA], and an actin cross-linking domain [ACD]). Biotype 1 isolates harbor MARTXVvtoxin types I and II, biotype 2 isolates carry MARTXVvtoxin type III, and biotype 3 isolates have MARTXVvtoxin type II. The analyzed biotype 2 isolates harbor two identical copies ofrtxA1, one chromosomal and the other plasmidic. The evolutionary history of the gene demonstrates that MARTXVvtoxins are mosaics, comprising pieces with different evolutionary histories, some of which have been acquired by intra- or interspecific horizontal gene transfer. Finally, we have found evidence that the evolutionary history of thertxA1gene for biotype 2 differs totally from the gene history of biotypes 1 and 3.
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8

Das, Debanu, Wang-Sik Lee, Joanna C. Grant, Hsiu-Ju Chiu, Carol L. Farr, Julie Vance, Heath E. Klock, et al. "Structure and Function of the DUF2233 Domain in Bacteria and in the Human Mannose 6-Phosphate Uncovering Enzyme." Journal of Biological Chemistry 288, no. 23 (April 9, 2013): 16789–99. http://dx.doi.org/10.1074/jbc.m112.434977.

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DUF2233, a domain of unknown function (DUF), is present in many bacterial and several viral proteins and was also identified in the mammalian transmembrane glycoprotein N-acetylglucosamine-1-phosphodiester α-N-acetylglucosaminidase (“uncovering enzyme” (UCE)). We report the crystal structure of BACOVA_00430, a 315-residue protein from the human gut bacterium Bacteroides ovatus that is the first structural representative of the DUF2233 protein family. A notable feature of this structure is the presence of a surface cavity that is populated by residues that are highly conserved across the entire family. The crystal structure was used to model the luminal portion of human UCE (hUCE), which is involved in targeting of lysosomal enzymes. Mutational analysis of several residues in a highly conserved surface cavity of hUCE revealed that they are essential for function. The bacterial enzyme (BACOVA_00430) has ∼1% of the catalytic activity of hUCE toward the substrate GlcNAc-P-mannose, the precursor of the Man-6-P lysosomal targeting signal. GlcNAc-1-P is a poor substrate for both enzymes. We conclude that, for at least a subset of proteins in this family, DUF2233 functions as a phosphodiester glycosidase.
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9

Sikela, James M., and Frans van Roy. "Changing the name of the NBPF/DUF1220 domain to the Olduvai domain." F1000Research 6 (July 17, 2018): 2185. http://dx.doi.org/10.12688/f1000research.13586.2.

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We are jointly proposing a new name for a protein domain of approximately 65 amino acids that has been previously termed NBPF or DUF1220. Our two labs independently reported the initial studies of this domain, which is encoded almost entirely within a single gene family. The name Neuroblastoma Breakpoint Family (NBPF) was applied to this gene family when the first identified member of the family was found to be interrupted in an individual with neuroblastoma. Prior to this discovery, the Pfam database had termed the domain DUF1220, denoting it as one of many protein domains of unknown function. It has been Pfam’s intention to use “DUF” nomenclature to serve only as a temporary placeholder until more appropriate names are proposed based on research findings. We believe that additional studies of this domain, primarily from our laboratories over the past 10 years, have resulted in furthering our understanding of these sequences to the point where proposing a new name for this domain is warranted. Because of considerable data linking the domain to human-specific evolution, brain expansion and cognition, we believe a name reflecting these findings would be appropriate. With this in mind, we have chosen to name the domain (and the repeat that encodes it) Olduvai. The gene family will remain as NBPF for now. The primary domain subtypes will retain their previously assigned names (e.g. CON1-3; HLS1-3), and the three-domain block that expanded dramatically in the human lineage will be termed the Olduvai triplet. The new name refers to Olduvai Gorge, which is a site in East Africa that has been the source of major anthropological discoveries in the early-mid 1900’s. We also chose the name as a tribute to the scientists who made important contributions to the early studies of human origins and our African genesis.
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10

Nurmemmedov, Elmar, and Santosh Kesari. "DDRE-11. DEVELOPMENT OF THE FIRST-IN-CLASS INHIBITOR OF CHD4 - SENSITIZING RESISTANT GLIOMAS." Neuro-Oncology 22, Supplement_2 (November 2020): ii63. http://dx.doi.org/10.1093/neuonc/noaa215.256.

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Abstract Glioblastoma is a lethal brain tumor with high recurrence rate. CHD4 overexpression, which drives resistance to DNA damage, is one of the major sources of recurrence. Since standard GBM treatments like radiation and temozolomide chemotherapy create DNA damage, inhibition of CHD4 offers a new therapeutic option for resensitizing GBM. CHD4 is a ubiquitously expressed ATP-dependent chromatin remodeler, which plays a crucial role in epigenetic regulation of gene expression and in DNA damage repair. Structurally, CHD4 contains an HMG-like domain, PHD domains, two chromodomains, a catalytic ATPase module, two domains of unknown function (DUF) and a C-terminal domain CHDCT2. Currently, no specific inhibitors targeting this chromatin remodeler have been reported yet. We aim to develop the first-in-class inhibitor targeting chromo-domain of CHD4. We have performed in silico screens to identify small molecules binding to the chromo-domains of CHD4. We present our growing in vitro data demonstrating biophysical properties and mechanism-of-action of these novel inhibitors. We expect that the experiments proposed here will result in the development of the first-in-class CHD4 inhibitor which can be used in the future not only to better study the physiological role of CHD4 but also to determine its potential as a novel targeted therapy for GBM.
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Dissertations / Theses on the topic "Domain of Unknown Function (DUF) 579"

1

Herliana, Lina. "Heterologous Expression and Functional Analysis of Plantago GT61 and DUF579 Genes in Arabidopsis thaliana." Thesis, 2017. http://hdl.handle.net/2440/121634.

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Mucilage released from Plantago ovata seed (psyllium) has been used for maintaining human health as a dietary fibre supplement. Heteroxylan is the main component, and its substitution affects solubility and viscosity of the end product. However, little is known about genes involved in xylan substitution so phylogenetic and transcript information were used to identify candidate genes in the GT61 and DUF579 families and their functions were tested in the model plant Arabidopsis thaliana. Plantago GT61_7, driven by a seed-coat promoter (ProDP1) was transformed into Arabidopsis using a floral dip and spray method. Ruthenium red staining of wild-type and T2 seeds from multiple independent transgenic lines showed a significant difference in the thickness of the adherent mucilage layer. The difference in mucilage phenotype suggests that GT61_7 may have a role in xylan substitution that affects seed coat adherence. This preliminary result needs to be examined using immunolabeling and monosaccharide analysis. For the DUF579 gene AT1G71690, a genome editing approach was adopted. Three single guide RNAs were designed using online tools and in silico analysis was performed to predict any changes in coding and protein sequences by each guide RNA. To test them in vitro, the CRISPR/Cas9 constructs were successfully delivered to protoplast cells using the Transient Expression in Arabidopsis Mesophyll Protoplast (TEAMP) method. However, an analysis using Tracking of Indels by Decomposition(TIDE) showed no evidence of edits in the DUF569 genomic DNA extracted from the protoplasts. Increasing the transfection efficiency or redesigning the sgRNA could lead to improved CRISPR/Cas9 activity.
Thesis (M.Bio.(PB)) -- University of Adelaide, Masters of Biotechnology (Plant Biotechnology), School of Agriculture, Food and Wine, 2017.
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