Journal articles on the topic 'Domain of Unknown Function (DUF) 579'
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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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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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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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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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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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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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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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Sikela, James M., and Frans van Roy. "A proposal to change the name of the NBPF/DUF1220 domain to the Olduvai domain." F1000Research 6 (December 28, 2017): 2185. http://dx.doi.org/10.12688/f1000research.13586.1.
Full textAbstract:
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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Gatti, Jean-Luc, Maya Belghazi, Fabrice Legeai, Marc Ravallec, Marie Frayssinet, Stéphanie Robin, Djibril Aboubakar-Souna, et al. "Proteo-Trancriptomic Analyses Reveal a Large Expansion of Metalloprotease-Like Proteins in Atypical Venom Vesicles of the Wasp Meteorus pulchricornis (Braconidae)." Toxins 13, no. 7 (July 19, 2021): 502. http://dx.doi.org/10.3390/toxins13070502.
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Meteorus pulchricornis (Ichneumonoidea, Braconidae) is an endoparasitoid wasp of lepidopteran caterpillars. Its parasitic success relies on vesicles (named M. pulchricornis Virus-Like Particles or MpVLPs) that are synthesized in the venom gland and injected into the parasitoid host along with the venom during oviposition. In order to define the content and understand the biogenesis of these atypical vesicles, we performed a transcriptome analysis of the venom gland and a proteomic analysis of the venom and purified MpVLPs. About half of the MpVLPs and soluble venom proteins identified were unknown and no similarity with any known viral sequence was found. However, MpVLPs contained a large number of proteins labelled as metalloproteinases while the most abundant protein family in the soluble venom was that of proteins containing the Domain of Unknown Function DUF-4803. The high number of these proteins identified suggests that a large expansion of these two protein families occurred in M. pulchricornis. Therefore, although the exact mechanism of MpVLPs formation remains to be elucidated, these vesicles appear to be “metalloproteinase bombs” that may have several physiological roles in the host including modifying the functions of its immune cells. The role of DUF4803 proteins, also present in the venom of other braconids, remains to be clarified.
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Araujo, Ana Claudia Guerra, Patricia Messenberg Guimaraes, Ana Paula Zotta Mota, Larissa Arrais Guimaraes, Bruna Medeiros Pereira, Christina Cleo Vinson, Ana Luíza Lacerda, Andressa Cunha Quintana Martins, and Ana Cristina Miranda Brasileiro. "Overexpression of DUF538 from Wild Arachis Enhances Plant Resistance to Meloidogyne spp." Agronomy 11, no. 3 (March 16, 2021): 559. http://dx.doi.org/10.3390/agronomy11030559.
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DUF538 proteins belong to a large group of uncharacterized protein families sharing the highly conserved Domain of Unknown Function (DUF). Attention has been given to DUF538 domain-containing proteins due to changes in their gene expression behavior and protein abundance during plant development and responses to stress. Putative roles attributed to DUF538 in plants under abiotic and biotic constraints include involvement in cell redox balance, chlorophyll breakdown and pectin degradation. Our previous transcriptome studies suggested that DUF538 is also involved in the resistance responses of wild Arachis species against the highly hazardous root-knot nematodes (RKNs). To clarify the role of the AsDUF538 gene from the wild peanut relative Arachis stenosperma in this interaction, we analyzed the effect of its overexpression on RKN infection in peanut and soybean hairy roots and Arabidopsis transgenic plants. AsDUF538 overexpression significantly reduced the infection in all three heterologous plant systems against their respective RKN counterparts. The distribution of AsDUF538 transcripts in RKN-infected Arachis roots and the effects of AsDUF538 overexpression on hormonal pathways and redox system in transgenic Arabidopsis were also evaluated. This is the first time that a DUF538 gene is functionally validated in transgenic plants and the earliest report on its role in plant defense against RKNs.
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Urbanowicz, B. R., M. J. Pena, S. Ratnaparkhe, U. Avci, J. Backe, H. F. Steet, M. Foston, et al. "4-O-methylation of glucuronic acid in Arabidopsis glucuronoxylan is catalyzed by a domain of unknown function family 579 protein." Proceedings of the National Academy of Sciences 109, no. 35 (August 14, 2012): 14253–58. http://dx.doi.org/10.1073/pnas.1208097109.
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Glantz, Spencer T., Erin E. Berlew, Zaynab Jaber, Benjamin S. Schuster, Kevin H. Gardner, and Brian Y. Chow. "Directly light-regulated binding of RGS-LOV photoreceptors to anionic membrane phospholipids." Proceedings of the National Academy of Sciences 115, no. 33 (July 31, 2018): E7720—E7727. http://dx.doi.org/10.1073/pnas.1802832115.
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We report natural light–oxygen–voltage (LOV) photoreceptors with a blue light-switched, high-affinity (KD ∼ 10−7 M), and direct electrostatic interaction with anionic phospholipids. Membrane localization of one such photoreceptor, BcLOV4 from Botrytis cinerea, is directly coupled to its flavin photocycle, and is mediated by a polybasic amphipathic helix in the linker region between the LOV sensor and its C-terminal domain of unknown function (DUF), as revealed through a combination of bioinformatics, computational protein modeling, structure–function studies, and optogenetic assays in yeast and mammalian cell line expression systems. In model systems, BcLOV4 rapidly translocates from the cytosol to plasma membrane (∼1 second). The reversible electrostatic interaction is nonselective among anionic phospholipids, exhibiting binding strengths dependent on the total anionic content of the membrane without preference for a specific headgroup. The in vitro and cellular responses were also observed with a BcLOV4 homolog and thus are likely to be general across the dikarya LOV class, whose members are associated with regulator of G-protein signaling (RGS) domains. Natural photoreceptors are not previously known to directly associate with membrane phospholipids in a light-dependent manner, and thus this work establishes both a photosensory signal transmission mode and a single-component optogenetic tool with rapid membrane localization kinetics that approaches the diffusion limit.
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Zhong, Hua, Hongyu Zhang, Rong Guo, Qiang Wang, Xiaoping Huang, Jianglin Liao, Yangsheng Li, Yingjin Huang, and Zhaohai Wang. "Characterization and Functional Divergence of a Novel DUF668 Gene Family in Rice Based on Comprehensive Expression Patterns." Genes 10, no. 12 (November 28, 2019): 980. http://dx.doi.org/10.3390/genes10120980.
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The domain of unknown function (DUF) superfamily encodes proteins of unknown functions in plants. Among them, DUF668 family members in plants possess a 29 amino-acid conserved domain, and this family has not been described previously. Here, we report this plant-specific novel DUF668 gene family containing 12 OsDUF668 genes in rice (Oryza sativa) and 91 DUF668s for the other seven plant species. In our study, DUF668 genes were present in both dicot and monocot plants, indicating that DUF668 is a conserved gene family that originated by predating the dicot–monocot divergence. Based on the gene structure and motif composition, the DUF668 family consists of two distinct clades, I and II in the phylogenetic tree. Remarkably, OsDUF668 genes clustered on the chromosomes merely show close phylogenetic relationships, suggesting that gene duplications or collinearity seldom happened. Cis-elements prediction display that over 80% of DUF668s contain phytohormone and light responsiveness factors. Further comprehensive experimental analyses of the OsDUF668 family are implemented in 22 different tissues, five hormone treatments, seven environmental factor stresses, and two pathogen-defense related stresses. The OsDUF668 genes express ubiquitously in analyzed rice tissues, and seven genes show tissue-specific high expression profiles. All OsDUF668s respond to drought, and some of Avr9/Cf-9 rapidly elicited genes resist to salt, wound, and rice blast with rapidly altered expression patterns. These findings imply that OsDUF668 is essential for drought-enduring and plant defense. Together, our results bring the important role of the DUF668 gene family in rice development and fitness to the fore.
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Zhao, Yan-Peng, Jian-Ling Shen, Wen-Jie Li, Na Wu, Chen Chen, and Yu-Xia Hou. "Evolutionary and Characteristic Analysis of RING-DUF1117 E3 Ubiquitin Ligase Genes in Gossypium Discerning the Role of GhRDUF4D in Verticillium dahliae Resistance." Biomolecules 11, no. 8 (August 3, 2021): 1145. http://dx.doi.org/10.3390/biom11081145.
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Verticillium wilt, primarily induced by the soil-borne fungus Verticillium dahliae, is a serious threat to cotton fiber production. There are a large number of really interesting new gene (RING) domain-containing E3 ubiquitin ligases in Arabidopsis, of which three (At2g39720 (AtRHC2A), At3g46620 (AtRDUF1), and At5g59550 (AtRDUF2)) have a domain of unknown function (DUF) 1117 domain in their C-terminal regions. This study aimed to detect and characterize the RDUF members in cotton, to gain an insight into their roles in cotton’s adaptation to environmental stressors. In this study, a total of 6, 7, 14, and 14 RDUF (RING-DUF1117) genes were detected in Gossypium arboretum, G. raimondii, G. hirsutum, and G. barbadense, respectively. These RDUF genes were classified into three groups. The genes in each group were highly conserved based on gene structure and domain analysis. Gene duplication analysis revealed that segmental duplication occurred during cotton evolution. Expression analysis revealed that the GhRDUF genes were widely expressed during cotton growth and under abiotic stresses. Many cis-elements related to hormone response and environment stressors were identified in GhRDUF promoters. The predicted target miRNAs and transcription factors implied that GhRDUFs might be regulated by gra-miR482c, as well as by transcription factors, including MYB, C2H2, and Dof. The GhRDUF genes responded to cold, drought, and salt stress and were sensitive to jasmonic acid, salicylic acid, and ethylene signals. Meanwhile, GhRDUF4D expression levels were enhanced after V. dahliae infection. Subsequently, GhRDUF4D was verified by overexpression in Arabidopsis and virus-induced gene silencing treatment in upland cotton. We observed that V. dahliae resistance was significantly enhanced in transgenic Arabidopsis, and weakened in GhRDUF4D silenced plants. This study conducted a comprehensive analysis of the RDUF genes in Gossypium, hereby providing basic information for further functional studies.
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Cao, Daomin, Peng Luo, and Shuangjie Peng. "The number of positive solutions to the Brezis-Nirenberg problem." Transactions of the American Mathematical Society 374, no. 3 (January 12, 2021): 1947–85. http://dx.doi.org/10.1090/tran/8287.
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In this paper we are concerned with the well-known Brezis-Nirenberg problem { − Δ u = u N + 2 N − 2 + ε u , a m p ; in Ω , u > 0 , a m p ; in Ω , u = 0 , a m p ; on ∂ Ω . \begin{equation*} \begin {cases} -\Delta u= u^{\frac {N+2}{N-2}}+\varepsilon u, &{\text {in}~\Omega },\\ u>0, &{\text {in}~\Omega },\\ u=0, &{\text {on}~\partial \Omega }. \end{cases} \end{equation*} The existence of multi-peak solutions to the above problem for small ε > 0 \varepsilon >0 was obtained (see Monica Musso and Angela Pistoia [Indiana Univ. Math. J. 51 (2002), pp. 541–579]). However, the uniqueness or the exact number of positive solutions to the above problem is still unknown. Here we focus on the local uniqueness of multi-peak solutions and the exact number of positive solutions to the above problem for small ε > 0 \varepsilon >0 . By using various local Pohozaev identities and blow-up analysis, we first detect the relationship between the profile of the blow-up solutions and Green’s function of the domain Ω \Omega and then obtain a type of local uniqueness results of blow-up solutions. Lastly we give a description of the number of positive solutions for small positive ε \varepsilon , which depends also on Green’s function.
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Husain, Mureed, Khawaja Ghulam Rasool, Muhammad Tufail, Waleed Saleh Alwaneen, and Abdulrahman Saad Aldawood. "RNAi-mediated silencing of vitellogenin gene curtails oogenesis in the almond moth Cadra cautella." PLOS ONE 16, no. 2 (February 11, 2021): e0245928. http://dx.doi.org/10.1371/journal.pone.0245928.
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Vitellogenins, major yolk protein precursors, play an essential role in the reproduction and spread of all oviparous species, including insects. To investigate reproductive strategies of the warehouse moth Cadra cautella at the molecular level, a partial transcript of the C. cautella vitellogenin (CcVg) gene was extended through the rapid amplification of cDNA ends PCR and sequenced. The complete CcVg mRNA transcript was 5,334 bp long, which encoded a protein of 1,778 amino acids, including the first 14 amino acids of the signal peptide. The deduced CcVg protein contained a putative cleavage site (RTRR) at the amino-terminal side, similar to several other insect species. DGQR and GI/LCG motifs were present at the CcVg gene C-terminus, followed by nine cysteine residues. CcVg harbored 131 putative phosphorylation sites, numbering 84, 19, and 28 sites for serine, threonine, and tyrosine, respectively. The transcript showed a great resemblance with other lepidopteran Vgs. CcVg protein analysis revealed three conserved regions: 1) vitellogenin-N domain, 2) DUF 1943 (domain of unknown function), and 3) a von Willebrand factor type D domain. Additionally, sex, stage-specific, and developmental expression profiles of the CcVg gene were determined through RT-PCR. The Vg was first expressed in 22-day-old female larvae, and its expression increased with growth. The phylogenetic analysis based on different insect Vgs revealed that the CcVg exhibited close ancestry with lepidopterans. The CcVg-based RNAi experiments were performed, and the effects were critically evaluated. The qRT-PCR results showed that CcVg-based dsRNA suppressed the Vg gene expression up to 90% at 48 h post-injection. Moreover, CcVg-based RNAi effects resulted in low fecundity and egg hatchability in the CcVg-based dsRNA-treated females. The females laid eggs, but because of insufficient yolk protein availability the eggs could not succeed to hatch. The significant difference in the fecundity and hatchability unveils the importance of CcVg gene silencing and confirmed that the Vg gene plays a key role in C. cautella reproduction and it has the potential to be used as a target for RNAi-mediated control of this warehouse pest.
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Mouton, Stijn, Kirill Ustyantsev, Frank Beltman, Lisa Glazenburg, and Eugene Berezikov. "TIM29 is required for enhanced stem cell activity during regeneration in the flatworm Macrostomum lignano." Scientific Reports 11, no. 1 (January 13, 2021). http://dx.doi.org/10.1038/s41598-020-80682-7.
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AbstractTIM29 is a mitochondrial inner membrane protein that interacts with the protein import complex TIM22. TIM29 was shown to stabilize the TIM22 complex but its biological function remains largely unknown. Until recently, it was classified as one of the Domain of Unknown Function (DUF) genes, with a conserved protein domain DUF2366 of unclear function. Since characterizing DUF genes can provide novel biological insight, we used previously established transcriptional profiles of the germline and stem cells of the flatworm Macrostomum lignano to probe conserved DUFs for their potential role in germline biology, stem cell function, regeneration, and development. Here, we demonstrate that DUF2366/TIM29 knockdown in M. lignano has very limited effect during the normal homeostatic condition but prevents worms from adapting to a highly proliferative state required for regeneration.
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"Catalytic Tales from Cryptic Sequences: Domain of Unknown Function (DUF)♦." Journal of Biological Chemistry 286, no. 31 (July 29, 2011): e99960-e99960. http://dx.doi.org/10.1074/jbc.p111.253260.
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Shu, Li, Neng Xiao, Jiong Qin, Qi Tian, Yanghui Zhang, Haoxian Li, Jing Liu, et al. "The Role of Microtubule Associated Serine/Threonine Kinase 3 Variants in Neurodevelopmental Diseases: Genotype-Phenotype Association." Frontiers in Molecular Neuroscience 14 (January 12, 2022). http://dx.doi.org/10.3389/fnmol.2021.775479.
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Objective: To prove microtubule associated serine/threonine kinase 3 (MAST3) gene is associated with neurodevelopmental diseases (NDD) and the genotype-phenotype correlation.Methods: Trio exome sequencing (trio ES) was performed on four NDD trios. Bioinformatic analysis was conducted based on large-scale genome sequencing data and human brain transcriptomic data. Further in vivo zebrafish studies were performed.Results: In our study, we identified four de novo MAST3 variants (NM_015016.1: c.302C > T:p.Ser101Phe; c.311C > T:p.Ser104Leu; c.1543G > A:p.Gly515Ser; and c.1547T > C:p.Leu516Pro) in four patients with developmental and epileptic encephalopathy (DEE) separately. Clinical heterogeneities were observed in patients carrying variants in domain of unknown function (DUF) and serine-threonine kinase (STK) domain separately. Using the published large-scale exome sequencing data, higher CADD scores of missense variants in DUF domain were found in NDD cohort compared with gnomAD database. In addition, we obtained an excess of missense variants in DUF domain when compared autistic spectrum disorder (ASD) cohort with gnomAD database, similarly an excess of missense variants in STK domain when compared DEE cohort with gnomAD database. Based on Brainspan datasets, we showed that MAST3 expression was significantly upregulated in ASD and DEE-related brain regions and was functionally linked with DEE genes. In zebrafish model, abnormal morphology of central nervous system was observed in mast3a/b crispants.Conclusion: Our results support the possibility that MAST3 is a novel gene associated with NDD which could expand the genetic spectrum for NDD. The genotype-phenotype correlation may contribute to future genetic counseling.
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Alam, SM Sabbir, M. Ruhul Amin, and M. Anwar Hossain. "In Silico Analysis: Annotations about Structural and Functional Features of DUF 2726 Family Member Proteins." Bangladesh Journal of Microbiology, June 25, 2016, 53–58. http://dx.doi.org/10.3329/bjm.v31i1.28466.
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Domains of unknown functions (DUFs) are a big set of protein families within the Pfam database that includes proteins of unknown function. In the absence of functional information, proteins are classified into different families based on conserved amino acid sequences and are potentially functionally important. In Pfam database, the numbers of families of DUFs are rapidly increasing and in current the fraction of DUF families had increased to about twenty two percent of all protein families. In this study we targeted DUF2726 member proteins which are mainly present in different bacterial species of Gamma-proteobacteria and have a particular domain organization. We analyzed the protein sequences of domain DUF2726 using different computational tools and databases. We found that this domain contains a nuclear localization signal peptide, which is conserved in Escherichia spp. and Shigella spp. It were also predicted that it has nucleic acid binding properties. Analyzing protein-protein interactions functional partners associated with DUF 2726 were revealed. Protein secondary structure, transmembrane helices structure were predicted. We have found that it has gene neighbourhood and co-occurrences with protein RepA and RepB. RepA and RepB are functionally associated with replication. RepA is a replication protein and RepB is a replication regulatory protein. Presence of a nucleic acid binding properties, a nuclear localization signal (NLS) signalling peptide, and possible interaction pattern with replication proteins, conjectures its possible role as a NLS like signalling peptide.Bangladesh J Microbiol, Volume 31, Number 1-2,June-Dec 2014, pp 53-58
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Higashitani, Atsushi, Toko Hashizume, Mai Takiura, Nahoko Higashitani, Mika Teranishi, Rika Oshima, Sachiko Yano, Kana Kuriyama, and Akira Higashibata. "Histone deacetylase HDA-4-mediated epigenetic regulation in space-flown C. elegans." npj Microgravity 7, no. 1 (September 1, 2021). http://dx.doi.org/10.1038/s41526-021-00163-7.
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AbstractEpigenetic changes during long-term spaceflight are beginning to be studied by NASA’s twin astronauts and other model organisms. Here, we evaluate the epigenetic regulation of gene expression in space-flown C. elegans by comparing wild type and histone deacetylase (hda)-4 mutants. Expression levels of 39 genes were consistently upregulated in all four generations of adult hda-4 mutants grown under microgravity compared with artificial Earth-like gravity (1G). In contrast, in the wild type, microgravity-induced upregulation of these genes occurred a little. Among these genes, 11 contain the domain of unknown function 19 (DUF-19) and are located in a cluster on chromosome V. When compared with the 1G condition, histone H3 trimethylation at lysine 27 (H3K27me3) increased under microgravity in the DUF-19 containing genes T20D4.12 to 4.10 locus in wild-type adults. On the other hand, this increase was also observed in the hda-4 mutant, but the level was significantly reduced. The body length of wild-type adults decreased slightly but significantly when grown under microgravity. This decrease was even more pronounced with the hda-4 mutant. In ground-based experiments, one of the T20D4.11 overexpressing strains significantly reduced body length and also caused larval growth retardation and arrest. These results indicate that under microgravity, C. elegans activates histone deacetylase HDA-4 to suppress overregulation of several genes, including the DUF-19 family. In other words, the expression of certain genes, including negative regulators of growth and development, is epigenetically fine-tuned to adapt to the space microgravity.
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"Structural and Functional Prediction of the Hypothetical Proteins from Pseudomonas Aeruginosa PA7." Archives of Infectious Diseases & Therapy 3, no. 2 (August 6, 2019). http://dx.doi.org/10.33140/aidt.03.02.3.
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Background & Aim: Pseudomonas aeruginosa is the most frequently isolated bacterium among those gram negative rods that are obligated aerobes. It is one of the important opportunistic human pathogens, causing severe chronic respiratory infection in patient with underlying conditions such as cystic fibrosis (CF) or bronchiectasis. The emergence of multi-drug resistance Pseudomonas aeruginosa strain in clinically isolated demands the development of better or new drugs against this pathogen. The study is to assign a precise function to hypothetical protein (HPs), whose functions are unknown. Materials and Methods: With the help of various bioinformatics tools, the extensive functional analysis of these hypothetical proteins was performed. This study combines a number of bioinformatics tools including Blastp, Pfam, InterProScan, SMART, PSLPred, CELLO, Signal Peptide, Expasy’s ProtParam tool, VirulenPred, VicmPred to gain information about the conserved regions, families, pathways, interactions, localizations and virulence related to particular protein. Result: The hypothetical proteins present in Pseudomonas Aeruginosa PA7 genome was extensively analyzed and annotated, out of 1350 hypothetical proteins, 25 proteins are catalytic domains, 31 proteins are enzymes, 46 proteins are integral membrane proteins, 72 proteins are transporters, 104 proteins are binding proteins, 404 proteins sequences contain a domain of unknown function (DUF), and 540 proteins cannot be functionally determined by any of the tools. Conclusion: Better understanding of the mechanism of pathogenesis and in finding novel therapeutic targets for Pseudomonas aeruginosa.
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Yuan, Guoqiang, Ting Zou, Zhiyuan He, Qiao Xiao, Gongwen Li, Sijing Liu, Pingping Xiong, et al. "SWOLLEN TAPETUM AND STERILITY 1 Is Required for Tapetum Degeneration and Pollen Wall Formation in Rice." Plant Physiology, June 24, 2022. http://dx.doi.org/10.1093/plphys/kiac307.
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Abstract The pollen wall is important for protecting the male gametophyte and for fertilization. The lipid components of the pollen wall are mainly synthesized and transported from the sporophytic tapetum. Although several factors related to lipid biosynthesis have been characterized, the molecular mechanisms underlying lipid biosynthesis during pollen development in rice (Oryza sativa L.) remain elusive. Here, we showed that mutation in the SWOLLEN TAPETUM AND STERILITY 1 (STS1) gene causes delayed tapetum degradation and aborted pollen wall formation in rice. STS1 encodes an endoplasmic reticulum (ER)-localized protein that contains domain of unknown function (DUF) 726 and exhibits lipase activity. Lipidomic and transcriptomic analyses showed that STS1 is involved in anther lipid homeostasis. Moreover, STS1 interacts with Polyketide Synthase 2 (OsPKS2) and Acyl-CoA Synthetase 12 (OsACOS12), two enzymes crucial in lipidic sporopollenin biosynthesis in pollen wall formation, suggesting a potentially lipidic metabolon for sporopollenin biosynthesis in rice. Collectively, our results indicate that STS1 is an important factor for lipid biosynthesis in reproduction, providing a target for the artificial control of male fertility in hybrid rice breeding and insight into the function of DUF726-containing protein in plants.
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Yang, Qi, Xiaocui Niu, Xiaona Tian, Xiujuan Zhang, Jingyu Cong, Ruigang Wang, Guosheng Zhang, and Guojing Li. "Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses." BMC Genomics 21, no. 1 (January 3, 2020). http://dx.doi.org/10.1186/s12864-019-6389-3.
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Abstract Background Domain of unknown function (DUF) proteins represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. The DUF4228 gene family is one of these families in plants that has not been described previously. Results In this study, we performed an extensive comparative analysis of DUF4228 proteins and determined their phylogeny in the plant lineage. A total of 489 high-confidence DUF4228 family members were identified from 14 land plant species, which sub-divided into three distinct phylogenetic groups: group I, group II and group III. A highly conserved DUF4228 domain and motif distribution existed in each group, implying their functional conservation. To reveal the possible biological functions of these DUF4228 genes, 25 ATDUF4228 sequences from Arabidopsis thaliana were selected for further analysis of characteristics such as their chromosomal position, gene duplications and gene structures. Ka/Ks analysis identified seven segmental duplication events, while no tandemly duplication gene pairs were found in A. thaliana. Some cis-elements responding to abiotic stress and phytohormones were identified in the upstream sequences of the ATDUF4228 genes. Expression profiling of the ATDUF4228 genes under abiotic stresses (mainly osmotic, salt and cold) and protein-protein interaction prediction suggested that some ATDUF4228 genes are may be involved in the pathways of plant resistance to abiotic stresses. Conclusion These results expand our knowledge of the evolution of the DUF4228 gene family in plants and will contribute to the elucidation of the biological functions of DUF4228 genes in the future.
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Tian, Xiaona, Xiaocui Niu, Ziru Chang, Xiujuan Zhang, Ruigang Wang, Qi Yang, and Guojing Li. "DUF1005 Family Identification, Evolution Analysis in Plants, and Primary Root Elongation Regulation of CiDUF1005 From Caragana intermedia." Frontiers in Genetics 13 (March 29, 2022). http://dx.doi.org/10.3389/fgene.2022.807293.
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Proteins with a domain of unknown function (DUF) represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. In particular, members of the DUF1005 family in plants have a 411-amino-acid conserved domain, and this family has not been described previously. In this study, a total of 302 high-confidence DUF1005 family members were identified from 58 plant species, and none were found in the four algae that were selected. Thus, this result showed that DUF1005s might belong to a kind of plant-specific gene family, and this family has not been evolutionarily expanded. Phylogenetic analysis showed that the DUF1005 family genes could be classified into four subgroups in 58 plant species. The earliest group to emerge was Group I, including a total of 100 gene sequences, and this group was present in almost all selected species spanning from mosses to seed plants. Group II and Group III, with 69 and 74 members, respectively, belong to angiosperms. Finally, with 59 members, Group IV was the last batch of genes to emerge, and this group is unique to dicotyledons. Expression pattern analysis of the CiDUF1005, a member of the DUF1005 family from Caragana intermedia, showed that CiDUF1005 genes were differentially regulated under various treatments. Compared to the wild type, transgenic lines with heterologous CiDUF1005 expression in Arabidopsis thaliana had longer primary roots and more lateral roots. These results expanded our knowledge of the evolution of the DUF1005 family in plants and will contribute to elucidating biological functions of the DUF1005 family in the future.