DOCSLIB.ORG

Supplementary Table 1

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

SUPPLEMENTARY TABLE I: Genes dysregulated with overexpression of HIF-2α in LP-1 cells. GeneID Gene Symbol Gene Name Fold Change Regulation in LP-1-HIF2A NM_001430 EPAS1 endothelial PAS domain protein 1/hypoxia-inducible factor 2α 40.71 up NM_001295 CCR1 chemokine (C-C motif) receptor 1 6.48 up NM_001010923 THEMIS thymocyte selection associated 5.14 up NM_000609 CXCL12 chemokine (C-X-C motif) ligand 12 4.65 up NM_017738 CNTLN centlein, centrosomal protein 4.03 up NM_001012301 ARSI arylsulfatase family, member I 3.99 up 10628 TXNIP thioredoxin interacting protein 3.81 up NM_003633 ENC1 ectodermal-neural cortex 1 (with BTB domain) 3.38 up NM_000351 STS steroid sulfatase (microsomal), isozyme S 3.23 up NM_007315 STAT1 signal transducer and activator of transcription 1 3.19 up NM_001175 ARHGDIB Rho GDP dissociation inhibitor (GDI) beta 3.14 up NM_021982 SEC24A SEC24 family member A 3.04 up NM_001876 CPT1A carnitine palmitoyltransferase 1A 3.01 up 57226 LYRM2 LYR motif containing 2 2.99 up NM_019058 DDIT4 DNA-damage-inducible transcript 4 2.96 up NM_004419 DUSP5 dual specificity phosphatase 5 2.88 up NM_021623 PLEKHA2 pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 2 2.74 up NM_022350 ERAP2 endoplasmic reticulum aminopeptidase 2 2.73 up NM_005779 LHFPL2 lipoma HMGIC fusion partner-like 2 2.68 up NM_197947 CLEC7A C-type lectin domain family 7, member A 2.67 up ENST00000334286 EDNRB endothelin receptor type B 2.62 up AK289800 SLC35D1 solute carrier family 35 (UDP-GlcA/UDP-GalNAc transporter), member D1 2.60 up NM_001866 COX7B cytochrome c oxidase subunit VIIb 2.60 up NM_001584 MPPED2 metallophosphoesterase domain containing 2 2.58 up XM_937293 ANKRD11 ankyrin repeat domain 11 2.49 up 348487 FAM131C family with sequence similarity 131, member C 2.49 up NM_002154 HSPA4 heat shock 70kDa protein 4 2.48 up NM_005606 LGMN legumain 2.44 up NM_025216 WNT10A wingless-type MMTV integration site family, member 10A 2.42 up NM_152289 ZNF561/ZNF562 zinc finger protein 561/zinc finger protein 562 2.41 up NM_002610 PDK1 pyruvate dehydrogenase kinase, isozyme 1 2.40 up NM_001008701 LPHN1 latrophilin 1 2.38 up NM_207459 TEX19 testis expressed 19 2.37 up NM_001144 AMFR autocrine motility factor receptor, E3 ubiquitin protein ligase 2.32 up NM_002287 LAIR1 leukocyte-associated immunoglobulin-like receptor 1 2.31 up NM_002119 HLA-DOA major histocompatibility complex, class II, DO alpha 2.30 up NM_001903 CTNNA1 catenin (cadherin-associated protein), alpha 1 2.27 up NM_012288 TRAM2 translocation associated membrane protein 2 2.26 up NM_004566 PFKFB3 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 2.25 up NM_000917 P4HA1 prolyl 4-hydroxylase, alpha polypeptide I 2.25 up NM_001099432 BCAS3 breast carcinoma amplified sequence 3 2.24 up NR_003006 SCARNA6 small Cajal body-specific RNA 6 2.24 up NM_006618 KDM5B lysine (K)-specific demethylase 5B 2.24 up GeneID Gene Symbol Gene Name Fold Change Regulation in LP-1-HIF2A NM_018433 KDM3A lysine (K)-specific demethylase 3A 2.23 up NM_052916 RNF157 ring finger protein 157 2.23 up NM_177401 MIDN midnolin 2.22 up NM_006290 TNFAIP3 tumor necrosis factor, alpha-induced protein 3 2.21 up NM_002906 RDX radixin 2.21 up NM_006227 PLTP phospholipid transfer protein 2.19 up NM_004910 PITPNM1 phosphatidylinositol transfer protein, membrane-associated 1 2.19 up NM_017751 SMPD4 sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3) 2.18 up NM_014488 RAB30 RAB30, member RAS oncogene family 2.18 up BC035599 C2CD3 C2 calcium-dependent domain containing 3 2.18 up 54587 MXRA8 matrix-remodelling associated 8 2.17 up 0 ZNF865 zinc finger protein 865 2.17 up NM_001040455 SIDT2 SID1 transmembrane family, member 2 2.13 up NM_213560 PKN1 protein kinase N1 2.12 up NM_001013840 TCTN3 tectonic family member 3 2.12 up BC019669 EEF1A1 eukaryotic translation elongation factor 1 alpha 1 2.11 up NM_003387 WIPF1 WAS/WASL interacting protein family, member 1 2.09 up BC005028 PLCXD1 phosphatidylinositol-specific phospholipase C, X domain containing 1 2.08 up NM_004199 P4HA2 prolyl 4-hydroxylase, alpha polypeptide II 2.06 up NM_145059 FUK fucokinase 2.05 up XM_938688 LOC101927789 putative ubiquitin-like protein FUBI-like protein ENSP00000310146-like 2.05 up NM_003900 SQSTM1 sequestosome 1 2.04 up NM_001007073 RPL32 ribosomal protein L32 2.04 up NM_022478 CDH24 cadherin 24, type 2 2.04 up NM_018427 RRN3 RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae) 2.04 up NM_018712 ELMOD1 ELMO/CED-12 domain containing 1 2.04 up NM_006480 RGS14 regulator of G-protein signaling 14 2.03 up 493 ATP2B4 ATPase, Ca++ transporting, plasma membrane 4 2.02 up NM_012292 HMHA1 histocompatibility (minor) HA-1 2.02 up NM_018343 RIOK2 RIO kinase 2 2.02 up NM_001037633 SIL1 SIL1 nucleotide exchange factor 2.02 up NM_016170 TLX2 T-cell leukemia homeobox 2 2.02 up NM_024503 HIVEP3 human immunodeficiency virus type I enhancer binding protein 3 2.02 up NM_000112 SLC26A2 solute carrier family 26 (anion exchanger), member 2 2.01 up BC036925 HARBI1 harbinger transposase derived 1 2.00 up NM_016113 TRPV2 transient receptor potential cation channel, subfamily V, member 2 2.00 up NM_001182 ALDH7A1 aldehyde dehydrogenase 7 family, member A1 7.88 down 57823 SLAMF7 SLAM family member 7 5.25 down NM_002966 S100A10 S100 calcium binding protein A10 4.87 down NM_005952 MT1X metallothionein 1X 3.58 down NM_001002858 ANXA2 annexin A2 3.52 down NM_052966 FAM129A family with sequence similarity 129, member A 3.26 down NM_031479 INHBE inhibin, beta E 3.17 down NM_178012 TUBB2B tubulin, beta 2B class IIb 3.16 down GeneID Gene Symbol Gene Name Fold Change Regulation in LP-1-HIF2A NM_005045 RELN reelin 3.07 down NM_206953 PRAME preferentially expressed antigen in melanoma 3.07 down NM_005620 S100A11 S100 calcium binding protein A11 3.06 down NM_017918 CCDC109B coiled-coil domain containing 109B 3.06 down NM_001336 CTSZ cathepsin Z 2.97 down NM_058179 PSAT1 phosphoserine aminotransferase 1 2.93 down NM_007069 PLA2G16 phospholipase A2, group XVI 2.90 down NM_006745 MSMO1 methylsterol monooxygenase 1 2.88 down --- ZNF626 zinc finger protein 626 2.86 down NM_015535 SPATS2L spermatogenesis associated, serine-rich 2-like 2.84 down NM_014278 HSPA4L heat shock 70kDa protein 4-like 2.82 down NM_018248 NEIL3 nei endonuclease VIII-like 3 2.77 down NM_024642 GALNT12 polypeptide N-acetylgalactosaminyltransferase 12 2.73 down NM_021021 SNTB1 syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1) 2.62 down BC007034 MT2A metallothionein 2A 2.50 down NM_015954 DERA deoxyribose-phosphate aldolase (putative) 2.49 down NM_198336 INSIG1 insulin induced gene 1 2.48 down NM_017878 HRASLS2 HRAS-like suppressor 2 2.45 down NM_016234 ACSL5 acyl-CoA synthetase long-chain family member 5 2.44 down NM_133436 ASNS asparagine synthetase (glutamine-hydrolyzing) 2.41 down NM_000507 FBP1 fructose-1,6-bisphosphatase 1 2.41 down NM_001100878 MROH6 maestro heat-like repeat family member 6 2.38 down NM_170710 WDR17 WD repeat domain 17 2.37 down 0 C4orf46 chromosome 4 open reading frame 46 2.36 down NM_015393 PARM1 prostate androgen-regulated mucin-like protein 1 2.31 down NM_144716 CCDC12 coiled-coil domain containing 12 2.29 down NM_004362 CLGN calmegin 2.29 down NM_002129 HMGB2 high mobility group box 2 2.28 down NM_052969 RPL39L ribosomal protein L39-like 2.28 down BC051726 GLUL glutamate-ammonia ligase 2.27 down NM_182943 PLOD2 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 2.26 down NM_024629 CENPU centromere protein U 2.25 down NM_004095 EIF4EBP1 eukaryotic translation initiation factor 4E binding protein 1 2.25 down NM_033429 CALML4 calmodulin-like 4 2.25 down NM_020961 METTL14 methyltransferase like 14 /// methyltransferase like 14 2.22 down NM_032117 MND1 meiotic nuclear divisions 1 homolog 2.22 down NM_032333 FAM213A family with sequence similarity 213, member A 2.22 down NM_024299 PPDPF pancreatic progenitor cell differentiation and proliferation factor 2.20 down 200810 ALG1L ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase-like 2.20 down NM_000712 BLVRA biliverdin reductase A 2.20 down NM_016303 WBP5 WW domain binding protein 5 2.18 down NR_001566 TERC telomerase RNA component 2.16 down --- FBXO25 F-box protein 25 2.16 down NM_000690 ALDH2 aldehyde dehydrogenase 2 family 2.14 down GeneID Gene Symbol Gene Name Fold Change Regulation in LP-1-HIF2A NM_000027 AGA aspartylglucosaminidase 2.14 down NM_138414 CCDC101 coiled-coil domain containing 101 2.14 down NM_021052 HIST1H2AB histone cluster 1, H2ab 2.13 down BC032672 HVCN1 hydrogen voltage-gated channel 1 2.13 down NM_145254 TMEM170A transmembrane protein 170A 2.12 down NM_004794 RAB33A RAB33A, member RAS oncogene family 2.12 down L20860 SEPT5-GP1BB SEPT5-GP1BB readthrough 2.11 down NM_018224 COA1 cytochrome c oxidase assembly factor 1 homolog 2.11 down NM_001085399 RELL1 RELT-like 1 2.11 down NM_147147 BVES blood vessel epicardial substance 2.11 down NM_031903 MRPL32 mitochondrial ribosomal protein L32 2.10 down NM_020192 YAE1D1 Yae1 domain containing 1 2.10 down NM_018569 AP1AR adaptor-related protein complex 1 associated regulatory protein 2.10 down NM_003360 UGT8 UDP glycosyltransferase 8 2.09 down NM_001100626 ERLIN1 ER lipid raft associated 1 2.08 down NM_145740 GSTA1 glutathione S-transferase alpha 1 2.08 down NM_001008393 C4orf46 chromosome 4 open reading frame 46 2.07 down NM_014051 TMEM14A transmembrane protein 14A 2.06 down NM_018010 IFT57 intraflagellar transport 57 homolog 2.06 down NM_021219 JAM2 junctional adhesion molecule 2 2.06
Recommended publications
  • The Diversity of Dolichol-Linked Precursors to Asn-Linked Glycans Likely Results from Secondary Loss of Sets of Glycosyltransferases

    The Diversity of Dolichol-Linked Precursors to Asn-Linked Glycans Likely Results from Secondary Loss of Sets of Glycosyltransferases

    The diversity of dolichol-linked precursors to Asn-linked glycans likely results from secondary loss of sets of glycosyltransferases John Samuelson*†, Sulagna Banerjee*, Paula Magnelli*, Jike Cui*, Daniel J. Kelleher‡, Reid Gilmore‡, and Phillips W. Robbins* *Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, 715 Albany Street, Boston, MA 02118-2932; and ‡Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester, MA 01665-0103 Contributed by Phillips W. Robbins, December 17, 2004 The vast majority of eukaryotes (fungi, plants, animals, slime mold, to N-glycans of improperly folded proteins, which are retained in and euglena) synthesize Asn-linked glycans (Alg) by means of a the ER by conserved glucose-binding lectins (calnexin͞calreticulin) lipid-linked precursor dolichol-PP-GlcNAc2Man9Glc3. Knowledge of (13). Although the Alg glycosyltransferases in the lumen of ER this pathway is important because defects in the glycosyltrans- appear to be eukaryote-specific, archaea and Campylobacter sp. ferases (Alg1–Alg12 and others not yet identified), which make glycosylate the sequon Asn and͞or contain glycosyltransferases dolichol-PP-glycans, lead to numerous congenital disorders of with domains like those of Alg1, Alg2, Alg7, and STT3 (1, 14–16). glycosylation. Here we used bioinformatic and experimental Protists, unicellular eukaryotes, suggest three notable exceptions methods to characterize Alg glycosyltransferases and dolichol- to the N-linked glycosylation path described in yeast and animals PP-glycans of diverse protists, including many human patho- (17). First, the kinetoplastid Trypanosoma cruzi (cause of Chagas gens, with the following major conclusions. First, it is demon- myocarditis), fails to glucosylate the dolichol-PP-linked precursor strated that common ancestry is a useful method of predicting and so makes dolichol-PP-GlcNAc2Man9 (18).
  • Fluorinated Mannosides Inhibit Cellular Fucosylation

    Fluorinated Mannosides Inhibit Cellular Fucosylation

    Fluorinated mannosides inhibit cellular fucosylation. Johan F.A. Pijnenborg[a],†, Emiel Rossing[a],†, Marek Noga[b], Willem Titulaer[a], Raisa Veizaj[c], Dirk J. Lefeber[b,c] and Thomas J. Boltje*[a] [a] J.F.A. Pijnenborg, E. Rossing, W. Titulaer, Dr. T.J. Boltje Department of Synthetic Organic Chemistry Institute for Molecules and Materials, Radboud University Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands [email protected] [b] Dr. M. Noga, Prof. D.J. Lefeber Department of Laboratory Medicine, Translational Metabolic Laboratory Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Geert Grooteplein Zuid 10, 6525GA, Nijmegen, The Netherlands [c] R. Veizaj, Prof. D.J. Lefeber Department of Neurology Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center Geert Grooteplein Zuid 10, 6525GA, Nijmegen, The Netherlands [†] These authors contributed equally to this work. Supporting information for this article is given via a link at the end of the document. Abstract: Fucose sugars are expressed on mammalian cell L-Fucose (Fuc) is a 6-deoxyhexose expressed at the termini of glycan membranes as part of glycoconjugates and mediates essential chains that decorate cell surface proteins and lipids.1 The fucose physiological processes. The aberrant expression of fucosylated residues on glycoconjugates are essential mediators of physiological glycans has been linked to pathologies such as cancer, inflammation, processes. For example, the fucose moiety in the tetrasaccharide infection, and genetic disorders. Tools to modulate fucose expression sialyl Lewisx (sLex) expressed on leukocytes is recognized by selectin on living cells are needed to elucidate the biological role of fucose receptors that regulate leukocyte recruitment and extravasation.
  • An Atpase Domain Common to Prokaryotic Cell Cycle Proteins

    An Atpase Domain Common to Prokaryotic Cell Cycle Proteins

    Proc. Natl. Acad. Sci. USA Vol. 89, pp. 7290-7294, August 1992 Biochemistry An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp7O heat shock proteins (structural comparison/property pattern/remote homology) PEER BORK, CHRIS SANDER, AND ALFONSO VALENCIA European Molecular Biology Laboratory, D-6900 Heidelberg, Federal Republic of Germany Communicated by Russell F. Doolittle, March 6, 1992 ABSTRACT The functionally diverse actin, hexokinase, and hsp7O protein families have in common an ATPase domain of known three-dimensional structure. Optimal superposition ofthe three structures and alignment ofmany sequences in each of the three families has revealed a set of common conserved residues, distributed in five sequence motifs, which are in- volved in ATP binding and in a putative interdomain hinge. From the multiple sequence aliment in these motifs a pattern of amino acid properties required at each position is defined. The discriminatory power of the pattern is in part due to the use of several known three-dimensional structures and many sequences and in part to the "property" method ofgeneralizing from observed amino acid frequencies to amino acid fitness at each sequence position. A sequence data base search with the pattern significantly matches sugar kinases, such as fuco-, glucono-, xylulo-, ribulo-, and glycerokinase, as well as the prokaryotic cell cycle proteins MreB, FtsA, and StbA. These are predicted to have subdomains with the same tertiary structure as the ATPase subdomains Ia and Ha of hexokinase, actin, and Hsc7O, a very similar ATP binding pocket, and the capacity for interdomain hinge motion accompanying func- tional state changes.
  • Physical Interactions Between the Alg1, Alg2, and Alg11 Mannosyltransferases of the Endoplasmic Reticulum

    Physical Interactions Between the Alg1, Alg2, and Alg11 Mannosyltransferases of the Endoplasmic Reticulum

    Glycobiology vol. 14 no. 6 pp. 559±570, 2004 DOI: 10.1093/glycob/cwh072 Advance Access publication on March 24, 2004 Physical interactions between the Alg1, Alg2, and Alg11 mannosyltransferases of the endoplasmic reticulum Xiao-Dong Gao2, Akiko Nishikawa1, and Neta Dean1 begins on the cytosolic face of the ER, where seven sugars (two N-acetylglucoseamines and five mannoses) are added 1Department of Biochemistry and Cell Biology, Institute for Cell and Developmental Biology, State University of New York, Stony Brook, sequentially to dolichyl phosphate on the outer leaflet of NY 11794-5215, and 2Research Center for Glycoscience, National the ER, using nucleotide sugar donors (Abeijon and Institute of Advanced Industrial Science and Technology, Tsukuba Hirschberg, 1992; Perez and Hirschberg, 1986; Snider and Downloaded from https://academic.oup.com/glycob/article/14/6/559/638968 by guest on 30 September 2021 Central 6, 1-1 Higashi, Tsukuba 305-8566, Japan Rogers, 1984). After a ``flipping'' or translocation step, the Received on January 26, 2004; revised on March 2, 2004; accepted on last seven sugars (four mannoses and three glucoses) are March 2, 2004 added within the lumen of the ER, using dolichol-linked sugar donors (Burda and Aebi, 1999). Once assembled, the The early steps of N-linked glycosylation involve the synthesis oligosaccharide is transferred from the lipid to nascent of a lipid-linked oligosaccharide, Glc3Man9GlcNAc2-PP- protein in a reaction catalyzed by oligosaccharyltransferase. dolichol, on the endoplasmic reticulum (ER) membrane. After removal of terminal glucoses and a single mannose, Prior to its lumenal translocation and transfer to nascent nascent glycoproteins bearing the N-linked Man8GlcNAc2 glycoproteins, mannosylation of Man5GlcNAc2-PP-dolichol core can exit the ER to the Golgi, where this core may is catalyzed by the Alg1, Alg2, and Alg11 mannosyltrans- undergo further carbohydrate modifications.
  • Clinical Utility Gene Card For: ALG1 Defective Congenital Disorder of Glycosylation

    Clinical Utility Gene Card For: ALG1 Defective Congenital Disorder of Glycosylation

    European Journal of Human Genetics (2015) 23, doi:10.1038/ejhg.2015.9 & 2015 Macmillan Publishers Limited All rights reserved 1018-4813/15 www.nature.com/ejhg CLINICAL UTILITY GENE CARD Clinical utility gene card for: ALG1 defective congenital disorder of glycosylation Jaak Jaeken*,1, Dirk Lefeber2 and Gert Matthijs3 European Journal of Human Genetics (2015) 23, doi:10.1038/ejhg.2015.9; published online 4 February 2015 1. DISEASE CHARACTERISTICS are known to the authors. The frequency and the prevalence of the 1.1 Name of the disease (synonyms) disease are not known. Deficiency of GDP-Man:GlcNAc2-PP-Dol mannosyltransferase, manno- syltransferase 1 deficiency, ALG1-CDG, CDG-Ik. 1.9 Diagnostic setting 1.2 OMIM# of the disease 608540 Yes No A. (Differential) diagnostics ⊠ ⊠ 1.3 Name of the analysed genes or DNA/chromosome segments: B. Predictive testing C. Risk assessment in relatives ⊠ □ ALG1. D. Prenatal ⊠ □ 1.4 OMIM# of the gene 605907. Comment: ALG1-CDG belongs to the five most common N-glycosylation 1.5 Mutational spectrum disorders together with PMM2-CDG, ALG6-CDG, MPI-CDG and Thirteen variants have been reported: ten missense variants, two SRD5A3-CDG. It is an autosomal recessive disease with a broad splicing variants and one deletion variant. The most frequent variant clinical spectrum, and with early death at the second day of life to – is c.773C4T(p.Ser258Leu)1–6 (www.lovd.nl/ALG1). The standard survival beyond the age of 20 years.1 10 Its phenotype is characterized reference sequence indicating reported variants (ENSG00000033011) by a predominant neurological involvement.
  • 1 ICR-Geneset Gene List

    1 ICR-Geneset Gene List

    ICR-geneset Gene List. IMAGE ID UniGene Locus Name Cluster 20115 Hs.62185 SLC9A6 solute carrier family 9 (sodium/hydrogen exchanger), isoform 6 21738 21899 Hs.78353 SRPK2 SFRS protein kinase 2 21908 Hs.79133 CDH8 cadherin 8, type 2 22040 Hs.151738 MMP9 matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase) 22411 Hs.183 FY Duffy blood group 22731 Hs.1787 PHRET1 PH domain containing protein in retina 1 22859 Hs.356487 ESTs 22883 Hs.150926 FPGT fucose-1-phosphate guanylyltransferase 22918 Hs.346868 EBNA1BP2 EBNA1 binding protein 2 23012 Hs.158205 BLZF1 basic leucine zipper nuclear factor 1 (JEM-1) 23073 Hs.284244 FGF2 fibroblast growth factor 2 (basic) 23173 Hs.151051 MAPK10 mitogen-activated protein kinase 10 23185 Hs.289114 TNC tenascin C (hexabrachion) 23282 Hs.8024 IK IK cytokine, down-regulator of HLA II 23353 23431 Hs.50421 RB1CC1 RB1-inducible coiled-coil 1 23514 23548 Hs.71848 Human clone 23548 mRNA sequence 23629 Hs.135587 Human clone 23629 mRNA sequence 23658 Hs.265855 SETMAR SET domain and mariner transposase fusion gene 23676 Hs.100841 Homo sapiens clone 23676 mRNA sequence 23772 Hs.78788 LZTR1 leucine-zipper-like transcriptional regulator, 1 23776 Hs.75438 QDPR quinoid dihydropteridine reductase 23804 Hs.343586 ZFP36 zinc finger protein 36, C3H type, homolog (mouse) 23831 Hs.155247 ALDOC aldolase C, fructose-bisphosphate 23878 Hs.99902 OPCML opioid binding protein/cell adhesion molecule-like 23903 Hs.12526 Homo sapiens clone 23903 mRNA sequence 23932 Hs.368063 Human clone 23932 mRNA sequence 24004
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
  • Supplementary Material Gram-Scale Production of Sugar Nucleotides And

    Supplementary Material Gram-Scale Production of Sugar Nucleotides And

    Electronic Supplementary Material (ESI) for Green Chemistry. This journal is © The Royal Society of Chemistry 2021 Supplementary Material Gram-scale production of sugar nucleotides and their derivatives Shuang Li[a]#, Shuaishuai Wang[b]#, Yaqian Wang[a], Jingyao Qu[c], Xian-wei Liu[a], Peng George Wang[d], and Junqiang Fang*[a] [a] Junqiang Fang, Shuang Li, Yaqian Wang, Xian-wei Liu National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Glycochemistry and Glycobiology, Shandong University, Qingdao, Shandong 266237, People’s Republic of China *Email: [email protected] [b] Shuaishuai Wang Department of Chemistry, George State University, Atlanta, GA, 30302-4098, US [c] Jingyao Qu State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, People’s Republic of China [d] Peng George Wang School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, People’s Republic of China # These authors contributed equally to this paper. I. Supplementary Figures..................................................................................................................................1 Figure S1. Effects of GlcNAc substrate concentration on conversion rate of UDP-GlcNAc......................1 Figure S2. Effect of buffer sytem on enzymatic conversion rate of UDP-GlcNAc.....................................1 Figure S3. Evaluation of recovery and recyclability of enzymes for UDP-GlcNAc...................................1 Table S1. Enzymes used in this work
  • Yeast Genome Gazetteer P35-65

    Yeast Genome Gazetteer P35-65

    gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal
  • Congenital Disorders of Glycosylation from a Neurological Perspective

    Congenital Disorders of Glycosylation from a Neurological Perspective

    brain sciences Review Congenital Disorders of Glycosylation from a Neurological Perspective Justyna Paprocka 1,* , Aleksandra Jezela-Stanek 2 , Anna Tylki-Szyma´nska 3 and Stephanie Grunewald 4 1 Department of Pediatric Neurology, Faculty of Medical Science in Katowice, Medical University of Silesia, 40-752 Katowice, Poland 2 Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; [email protected] 3 Department of Pediatrics, Nutrition and Metabolic Diseases, The Children’s Memorial Health Institute, W 04-730 Warsaw, Poland; [email protected] 4 NIHR Biomedical Research Center (BRC), Metabolic Unit, Great Ormond Street Hospital and Institute of Child Health, University College London, London SE1 9RT, UK; [email protected] * Correspondence: [email protected]; Tel.: +48-606-415-888 Abstract: Most plasma proteins, cell membrane proteins and other proteins are glycoproteins with sugar chains attached to the polypeptide-glycans. Glycosylation is the main element of the post- translational transformation of most human proteins. Since glycosylation processes are necessary for many different biological processes, patients present a diverse spectrum of phenotypes and severity of symptoms. The most frequently observed neurological symptoms in congenital disorders of glycosylation (CDG) are: epilepsy, intellectual disability, myopathies, neuropathies and stroke-like episodes. Epilepsy is seen in many CDG subtypes and particularly present in the case of mutations
  • NICU Gene List Generator.Xlsx

    NICU Gene List Generator.Xlsx

    Neonatal Crisis Sequencing Panel Gene List Genes: A2ML1 - B3GLCT A2ML1 ADAMTS9 ALG1 ARHGEF15 AAAS ADAMTSL2 ALG11 ARHGEF9 AARS1 ADAR ALG12 ARID1A AARS2 ADARB1 ALG13 ARID1B ABAT ADCY6 ALG14 ARID2 ABCA12 ADD3 ALG2 ARL13B ABCA3 ADGRG1 ALG3 ARL6 ABCA4 ADGRV1 ALG6 ARMC9 ABCB11 ADK ALG8 ARPC1B ABCB4 ADNP ALG9 ARSA ABCC6 ADPRS ALK ARSL ABCC8 ADSL ALMS1 ARX ABCC9 AEBP1 ALOX12B ASAH1 ABCD1 AFF3 ALOXE3 ASCC1 ABCD3 AFF4 ALPK3 ASH1L ABCD4 AFG3L2 ALPL ASL ABHD5 AGA ALS2 ASNS ACAD8 AGK ALX3 ASPA ACAD9 AGL ALX4 ASPM ACADM AGPS AMELX ASS1 ACADS AGRN AMER1 ASXL1 ACADSB AGT AMH ASXL3 ACADVL AGTPBP1 AMHR2 ATAD1 ACAN AGTR1 AMN ATL1 ACAT1 AGXT AMPD2 ATM ACE AHCY AMT ATP1A1 ACO2 AHDC1 ANK1 ATP1A2 ACOX1 AHI1 ANK2 ATP1A3 ACP5 AIFM1 ANKH ATP2A1 ACSF3 AIMP1 ANKLE2 ATP5F1A ACTA1 AIMP2 ANKRD11 ATP5F1D ACTA2 AIRE ANKRD26 ATP5F1E ACTB AKAP9 ANTXR2 ATP6V0A2 ACTC1 AKR1D1 AP1S2 ATP6V1B1 ACTG1 AKT2 AP2S1 ATP7A ACTG2 AKT3 AP3B1 ATP8A2 ACTL6B ALAS2 AP3B2 ATP8B1 ACTN1 ALB AP4B1 ATPAF2 ACTN2 ALDH18A1 AP4M1 ATR ACTN4 ALDH1A3 AP4S1 ATRX ACVR1 ALDH3A2 APC AUH ACVRL1 ALDH4A1 APTX AVPR2 ACY1 ALDH5A1 AR B3GALNT2 ADA ALDH6A1 ARFGEF2 B3GALT6 ADAMTS13 ALDH7A1 ARG1 B3GAT3 ADAMTS2 ALDOB ARHGAP31 B3GLCT Updated: 03/15/2021; v.3.6 1 Neonatal Crisis Sequencing Panel Gene List Genes: B4GALT1 - COL11A2 B4GALT1 C1QBP CD3G CHKB B4GALT7 C3 CD40LG CHMP1A B4GAT1 CA2 CD59 CHRNA1 B9D1 CA5A CD70 CHRNB1 B9D2 CACNA1A CD96 CHRND BAAT CACNA1C CDAN1 CHRNE BBIP1 CACNA1D CDC42 CHRNG BBS1 CACNA1E CDH1 CHST14 BBS10 CACNA1F CDH2 CHST3 BBS12 CACNA1G CDK10 CHUK BBS2 CACNA2D2 CDK13 CILK1 BBS4 CACNB2 CDK5RAP2
  • The Role of the Salvage Pathway in Nucleotide Sugar Biosynthesis

    The Role of the Salvage Pathway in Nucleotide Sugar Biosynthesis

    THE ROLE OF THE SALVAGE PATHWAY IN NUCLEOTIDE SUGAR BIOSYNTHESIS: IDENTIFICATION OF SUGAR KINASES AND NDP-SUGAR PYROPHOSPHORYLASES by TING YANG (Under the Direction of Maor Bar-Peled) ABSTRACT The synthesis of polysaccharides, glycoproteins, glycolipids, glycosylated secondary metabolites and hormones requires a large number of glycosyltransferases and a constant supply of nucleotide sugars. In plants, photosynthesis and the NDP-sugar inter-conversion pathway are the major entry points to form NDP-sugars. In addition to these pathways is the salvage pathway, a less understood metabolism that provides the flux of NDP-sugars. This latter pathway involves the hydrolysis of glycans to free sugars, sugar transport, sugar phosphorylation and nucleotidylation. The balance between glycan synthesis and recycling as well as its regulation at various plant developmental stages remains elusive as many of the molecular components are unknown. To understand how the salvage pathway contributes to the sugar flux and cell wall biosynthesis, my research focused on the functional identification of salvage pathway sugar kinases and NDP-sugar pyrophosphorylases. This research led to the first identification and enzymatic characterization of galacturonic acid kinase (GalA kinase), galactokinase (GalK), a broad UDP-sugar pyrophosphorylase (sloppy), two promiscuous UDP-GlcNAc pyrophosphorylases (GlcNAc-1-P uridylyltransferases), as well as UDP-sugar pyrophosphorylase paralogs from Trypanosoma cruzi and Leishmania major. To evaluate the salvage pathway in plant biology, we further investigated a sugar kinase mutant: galacturonic acid kinase mutant (galak) and determined if and how galak KO mutant affects the synthesis of glycans in Arabidopsis. Feeding galacturonic acid to the seedlings exhibited a 40-fold accumulation of free GalA in galak mutant, while the wild type (WT) plant readily metabolizes the fed-sugar.