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Supporting Information for Proteomics DOI 10.1002/Pmic.200600568

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Supporting Information for Proteomics DOI 10.1002/pmic.200600568 Xiao-Li Wang, Alex Fu, Sreekumar Raghavakaimal and Hon-Chi Lee Proteomic analysis of vascular endothelial cells in response to laminar shear stress ª 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com Table A. Proteins altereations after 10 minutes of shear stress Accesion # Protein Name H:L* Matched Sequence Charge Score Confidence % Error Peptide Number gi|39931056 1-deoxy-D-xylulose 5-phosphate reductoisomerase 1 (DXP reductoisomerase 1) 3.78 QNGCR 2 21 75 1.6 2 gi|14548081 28 kDa and 33 kDa Inner dynein arm light chain, axonemal (p28, p33) 2.86 CEAIEK 2 32 90 3.7 3 gi|1723793 3 beta-hydroxysteroid dehydrogenase 0.21 VKIVCAYR 2 28 90 5.9 2 gi|32171609 30S ribosomal protein S11 2.17 GCAHIK 2 33 90 6.2 4 gi|34222742 30S ribosomal protein S2 0.41 REYNAVAECHK 3 20 75 1.3 4 gi|26399495 30S ribosomal protein S5P 0.19 GCGSWEZGZGRPHTVALK 3 25 75 1 4 gi|3929352 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMG-CoA reductase) 0.07 GCSVITR 2 23 75 3.2 4 gi|23396668 3-isopropylmalate dehydratase small subunit (Isopropylmalate isomerase) 0.46 AAGVSCVIAK 2 25 75 1.3 3 gi|3123178 50S ribosomal protein L32 (Ribosomal protein I) (BL37) 2.17 ACGTYK 2 32 90 6.2 2 gi|135758 Acetyl-CoA acetyltransferase (Acetoacetyl-CoA thiolase) 0.31 VCASAMK 2 20 75 1.2 3 gi|14194435 ADAM 11 precursor (A disintegrin and metalloproteinase domain 11) 0.23 GSCGRK 2 24 75 4 2 gi|6174971 Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase) 2.86 GCAQALK 2 32 90 3.7 3 gi|3913952 Adenylate kinase (ATP-AMP transphosphorylase) 0.23 GTQCAK 2 20 75 0.6 4 gi|6647402 Alanine racemase 2.86 ECALQK 2 32 90 3.7 3 gi|730039 Alpha-1,3-mannosyltransferase MNN1 6.47 ASAGACGGYIWZATHK 3 33 90 0.8 2 gi|2497468 AP-1-like transcription factor 0.15 AKCSEK 2 20 75 3.8 3 gi|2498144 Apolipophorins precursor (Contains: APOLP-1; APOLP-2) 8.26 HCTDIK 2 26 75 1.1 2 gi|1351967 Aquaporin 4 (WCH4) (Mercurial-insensitive water channel) (MIWC) 0.26 ZGPPCSR 2 20 75 7.4 2 gi|13123999 Arginyl-tRNA--protein transferase 1 0.17 VFCAR 2 21 75 4 4 gi|17432914 ATP-binding cassette, sub-family G, member 8 (Sterolin-2) 2.86 QCANTR 2 32 90 3.7 3 gi|25090065 ATP-dependent helicase DDX1 (DEAD box protein 1) 0.19 HYSCVZLHGDRKPQER 3 25 75 1 4 gi|33112387 Axoneme-associated protein mst101(3) 2.86 KCAELAK 2 32 90 3.7 3 gi|5921178 Bloom's syndrome protein homolog (mBLM) 3.66 GGSTTCRK 2 22 75 3.6 3 gi|22095546 Cadherin EGF LAG seven-pass G-type receptor 1 precursor 2.86 AGCASQR 2 32 90 3.7 3 gi|20137454 Caspase recruitment domain protein 10 0.22 CLPSSR 2 20 75 7 2 gi|1350651 Chloroplast 50s ribosomal protein L4 0.46 EIYCG 2 23 75 5.2 2 gi|18202613 Chromosome-associated kinesin KLP1 (Chromokinesin) 3.71 MCGZRK 2 29 90 1.3 4 gi|119765 Coagulation factor VII (Serum prothrombin conversion accelerator) 0.28 SYIZFCPDGFEGR 3 22 75 2.3 2 gi|124411 Colicin M immunity protein (Microcin M immunity protein) 0.34 SCGDFMK 2 40 99 4.5 4 gi|117422 Crumbs protein precursor (95F) 0.27 CPNGYK 2 20 75 5.7 2 gi|1169263 Defensin 5.58 GGRCVNTIZNZR 3 24 75 0.8 3 gi|2494282 Delta-like protein 1 precursor (Drosophila Delta homolog 1) (Delta1) 9.39 GGSGPPCAZR 2 33 90 3.8 4 gi|1174738 DNA topoisomerase 2.86 CEHAQIK 2 32 90 3.7 3 gi|729352 DNA43 protein 0.15 CGSPINISLHK 2 41 99 6.3 3 gi|401016 DNA-directed RNA polymerase subunit A' 2.86 CEALEK 2 32 90 3.7 3 gi|137797 E7 protein 2.86 CEATLR 2 32 90 3.7 3 gi|119180 Elongation factor 3A (EF-3A) (EF-3) 0.02 YGIZGPNGCGK 2 20 75 3.6 2 gi|21264129 Excinuclease ABC subunit 0.22 CAGPZVK 2 22 75 6.5 2 gi|30581063 Fibulin-1 precursor (Basement-membrane protein 90) (BM-90) 0.42 ZZHZCMLGK 3 39 99 0.6 3 gi|113001 Filamin A (Alpha-filamin) (Filamin 1) (Endothelial actin-binding protein) 0.37 IVGPSGAAVPCK 2 33 90 2.1 4 gi|32129530 Filamin C (Gamma-filamin) 0.06 CSGPGLGAGVR 2 49 99 5.2 3 gi|3122339 Galectin-1 (Beta-galactoside-binding lectin L-14-I) 0.28 DDNNLCLHFNPR 3 24 75 2.3 3 gi|20138165 GC-rich sequence DNA-binding factor homolog 0.10 GERTISQLENFCR 3 21 75 2.1 3 gi|130466 Genome polyprotein 0.02 TCGAPPZR 2 22 75 2.3 4 gi|1169883 Glucocorticoid receptor (GR) 0.22 NCPAZR 2 20 75 7 2 gi|21759144 Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 0.17 FVCAR 2 21 75 4 4 gi|17380211 Glutamate 5-kinase (Gamma-glutamyl kinase) (GK) 2.86 QCAELK 2 32 90 3.7 3 gi|462162 Guanine nucleotide-binding protein alpha-4 subunit (G alpha 4) 0.06 EIVNCDYFK 3 43 99 0.9 2 gi|140581 H repeat-associated protein ydcC (ORF-H) 3.62 GKIITTDAMGCQK 3 26 75 2.2 2 gi|122134 H-2 class I histocompatibility antigen, q8 alpha chain precursor 3.71 ETLLCTDPPK 3 43 99 0.4 2 gi|399997 Homeobox protein Hox-B1 (Ghox-lab) 0.10 DPACPSEPZPNASRAR 3 21 75 2.1 3 gi|22001687 Homoserine kinase (HK) 0.03 CVSAVHR 2 22 75 1.8 2 gi|2498452 Imidazole glycerol phosphate synthase subunit hisF (IGP synthase cyclase subunit) 0.27 HTAVCG 2 22 75 0.4 4 gi|21431575 Insulin receptor-related protein precursor (IRR) 2.86 CEGLZPK 2 32 90 3.7 3 gi|26395479 Interleukin-1 receptor-like 2 precursor (IL-1Rrp2) 0.30 CNAATGLITP 2 24 75 1.6 2 gi|6016387 Isopenicillin N synthetase (IPNS) (Isopenicillin N synthase) 9.32 RZCZGASR 2 22 75 6.2 3 gi|6016488 L-lactate dehydrogenase C chain (LDH-C) (LDH testis subunit) (LDH-X) 0.45 VFGSGCNLDSAR 3 20 75 12.6 3 gi|38257899 LysM-domain GPI-anchored protein 2 precursor 0.26 ACSSSVRK 2 22 75 0.5 4 gi|1708892 Lysozyme precursor (1,4-beta-N-acetylmuramidase) 0.23 ASKCAK 2 20 75 0.6 4 gi|1718104 Major capsid protein (MCP) 2.86 ACGAGVNVK 2 32 90 3.7 3 gi|547903 Metabotropic glutamate receptor 6 precursor (mGluR6) 2.86 ACGALKK 2 32 90 3.7 3 gi|8928207 Metallothionein (MT) (AnMT) 0.20 GGSSEKCSZZN 3 22 75 0.4 2 gi|2497900 Metallothionein-like protein type 0.17 ZGSSCK 2 21 75 4 4 gi|2497517 Mevalonate kinase (MK) 0.02 IFNCRMMN 2 20 75 3.6 2 gi|24211982 Midasin (MIDAS-containing protein) 0.15 SZCSSK 2 20 75 2.1 2 gi|30315970 Mineralocorticoid receptor (MR) 0.22 NCPAZR 2 20 75 7 2 gi|139160 Morphogenetic protein (p12 protein) 5.85 KPEVEVQAAPFTCR 3 20 75 0.9 2 gi|38257869 NAD-dependent deacetylase (Regulatory protein SIR2 homolog) 3.71 CMGZER 2 29 90 1.3 4 gi|115422 Neural-cadherin precursor (N-cadherin) (Cadherin-2) 18.24 MCRIAGTPPR 3 52 99 4.8 3 gi|129168 Oncostatin M precursor (OSM) 3.78 LEGCR 2 21 75 1.6 2 gi|37999492 Patched protein homolog 2.43 NYFDVCPHIDR 3 30 90 4.4 4 gi|548630 Peptide transporter PTR2 (Peptide permease PTR2) 0.41 CWLIAIVELSER 3 20 75 1.3 4 gi|6919841 Phorbol-12-myristate-13-acetate-induced protein 1 (PMA-induced protein 1) 0.26 LFCSGT 2 21 75 5.4 3 gi|20139379 Phosphate-binding protein 3 precursor (PBP-3) (PstS-3) (Antigen Ag88) 0.08 VDCGGK 2 22 75 0.8 2 gi|24638082 Phospholipase A2 (Phosphatidylcholine 2-acylhydrolase) 0.15 FKHTDACZR 2 28 90 6.3 3 gi|130588 POL polyprotein [Contains: Reverse transcriptase ; Endonuclease] 0.42 RGAYCLWK 3 39 99 0.6 3 gi|112711 Potential 194 kDa protein (putative replicase) [contains: 134 kDa protein] 0.29 CNNTYQGZTZR 3 22 75 5.3 3 gi|30316371 Potential phospholipid-transporting ATPase ID (ATPase class I type 8B member 2) 4.48 MFCMK 2 27 75 5.4 4 gi|549719 Probable beta-adaptin (Clathrin assembly protein large beta chain) 0.46 TAVICVAK 2 20 75 1.3 4 gi|13124065 Probable calcium-binding mitochondrial carrier F55A11.4 3.71 EGIRCFYK 3 43 99 0.4 2 gi|13124698 Probable calcium-binding mitochondrial carrier YNL083W 3.78 LEGCR 2 21 75 1.6 2 gi|267105 Probable large tegument protein 0.29 TLLSICPK 2 25 75 3.1 4 gi|2495391 Probable nitrogen assimilation transcriptional activator 2.86 CGALTVK 2 32 90 3.7 3 gi|2833610 Probable precorrin-3B C17-methyltransferase (Precorrin-3 methyltransferase) 2.35 VDLIVCYK 2 26 75 2.3 2 gi|6647879 Probable tRNA modification GTPase trmE 4.19 AFVCVSAK 2 37 99 0.5 2 gi|2501463 Probable ubiquitin carboxyl-terminal hydrolase FAF-X 2.29 ILDYSCSQDR 3 35 99 4.5 4 gi|130976 Profilin 2.33 CYEMASHLR 3 23 75 4.3 2 gi|12644100 Progesterone receptor (PR) 0.22 NCPAZR 2 20 75 7 2 gi|730305 Prostaglandin-H2 D-isomerase precursor (Lipocalin-type prostaglandin D synthase) 0.46 FTAFCK 2 20 75 5.2 2 gi|400137 Protein kinase C, zeta type (nPKC-zeta) 0.35 GAYCGQZSER 2 36 99 4.9 3 gi|1718018 Protein U59 4.08 EMVSCIWK 3 57 99 0.5 4 gi|12230486 Protein-arginine deiminase type I (Peptidylarginine deiminase I) 0.17 VFCAR 2 21 75 4 4 gi|6226890 Protein-tyrosine phosphatase 0.37 QTTNCZYR 3 20 75 0.4 3 gi|37999834 Protocadherin gamma A9 precursor (PCDH-gamma-A9) 0.38 CLVNFK 2 24 75 11 3 gi|1345982 Putative FERT-1 protein 4.49 CGVALLPSGA 2 25 75 3.6 3 gi|6094277 Putative hexulose-6-phosphate isomerase (HUMPI) 2.25 MQEAGFIC 2 21 75 1.2 3 gi|1730602 Putative vitellogenin receptor precursor (Yolkless protein) (YL) 2.86 KCALGAK 2 32 90 3.7 3 gi|6685820 PyrBI protein 3.78 LEGVCR 2 21 75 1.6 2 gi|7388019 Pyruvate,phosphate dikinase (Pyruvate,orthophosphate dikinase) 2.86 QCALQK 2 32 90 3.7 3 gi|21903444 Raf homolog serine 0.26 CASSSIDR 2 22 75 0.5 4 gi|132608 Ribonucleoside-diphosphate reductase M1 chain ) 2.86 QCALISK 2 32 90 3.7 3 gi|37538006 RING-box protein 2 (Rbx2) (RING finger protein 7) 2.86 CQAENK 2 32 90 3.7 3 gi|1346520 S-adenosylmethionine synthetase 3.78 KNGTCR 2 21 75 1.6 2 gi|1346361 Serine/threonine-protein kinase shk2 0.46 TFCFK 2 20 75 5.2 2 gi|11387093 Serotonin N-acetyltransferase (Aralkylamine N-acetyltransferase) (AA-NAT) 0.22 CLPZAR 2 20 75 7 2 gi|136191 Serotransferrin precursor (Transferrin) 4.20 SVIPSDGPSVACVK 3 20 75 1 4 gi|6094381 SOX-15 protein (SOX-20 protein) (SOX-12 protein) 0.27 SSGAGPSRCGQGR 3 23 75 0.7 2 gi|19863446 Splicing factor 3B subunit 3 2.81
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  • Evolutionary Diversification and Characterization of the Eubacterial

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    Carretero-Paulet et al. BMC Evolutionary Biology 2013, 13:180 http://www.biomedcentral.com/1471-2148/13/180 RESEARCH ARTICLE Open Access Evolutionary diversification and characterization of the eubacterial gene family encoding DXR type II, an alternative isoprenoid biosynthetic enzyme Lorenzo Carretero-Paulet1,2*, Agnieszka Lipska1, Jordi Pérez-Gil3, Félix J Sangari4, Victor A Albert1 and Manuel Rodríguez-Concepción3* Abstract Background: Isoprenoids constitute a vast family of natural compounds performing diverse and essential functions in all domains of life. In most eubacteria, isoprenoids are synthesized through the methylerythritol 4-phosphate (MEP) pathway. The production of MEP is usually catalyzed by deoxyxylulose 5-phosphate reductoisomerase (DXR-I) but a few organisms use an alternative DXR-like enzyme (DXR-II). Results: Searches through 1498 bacterial complete proteomes detected 130 sequences with similarity to DXR-II. Phylogenetic analysis identified three well-resolved clades: the DXR-II family (clustering 53 sequences including eleven experimentally verified as functional enzymes able to produce MEP), and two previously uncharacterized NAD(P)-dependent oxidoreductase families (designated DLO1 and DLO2 for DXR-II-like oxidoreductases 1 and 2). Our analyses identified amino acid changes critical for the acquisition of DXR-II biochemical function through type-I functional divergence, two of them mapping onto key residues for DXR-II activity. DXR-II showed a markedly discontinuous distribution, which was verified at several levels: taxonomic (being predominantly found in Alphaproteobacteria and Firmicutes), metabolic (being mostly found in bacteria with complete functional MEP pathways with or without DXR-I), and phenotypic (as no biological/phenotypic property was found to be preferentially distributed among DXR-II-containing strains, apart from pathogenicity in animals).
  • Subunits Shared by Eukaryotic Nuclear RNA Polymerases

    Subunits Shared by Eukaryotic Nuclear RNA Polymerases

    Downloaded from genesdev.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Subunits shared by eukaryotic nuclear RNA polymerases Nancy A. Woychik, Sha-Mei Liao, Peter A. Kolodziej, and Richard A. Young Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142 USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 USA RNA polymerases I, II, and III share three subunits that are immunologically and biochemically indistinguishable. The Saccharomyces cerevisiae genes that encode these subunits (RPBS, RPB6, and RPBS) were isolated and sequenced, and their transcriptional start sites were deduced. RPB5 encodes a 25-kD protein, RPB6, an 18-kD protein, and RPB8, a 16-kD protein. These genes are single copy, reside on different chromosomes, and are essential for viability. The fact that the genes are single copy, corroborates previous evidence suggesting that each of the common subunits is identical in RNA polymerases I, II, and III. Furthermore, immunoprecipitation of RPB6 coprecipitates proteins whose sizes are consistent with RNA polymerase I, II, and III subunits. Sequence similarity between the yeast RPB5 protein and a previously characterized human RNA polymerase subunit demonstrates that the common subunits of the nuclear RNA polymerases are well conserved among eukaryotes. The presence of these conserved and essential subunits in all three nuclear RNA polymerases and the absence of recognizable sequence motifs for DNA and nucleoside triphosphate-binding indicate that the common subunits do not have a catalytic role but are important for a function shared by the RNA polymerases such as transcriptional efficiency, nuclear localization, enzyme stability, or coordinate regulation of rRNA, mRNA, and tRNA synthesis.
  • Targeting the RNA Polymerase I Transcription for Cancer Therapy Comes of Age

    Targeting the RNA Polymerase I Transcription for Cancer Therapy Comes of Age

    Targeting the RNA Polymerase I Transcription for Cancer Therapy Comes of Age Ferreira, R., Schneekloth, J. S., Panov, K. I., Hannan, K. M., & Hannan, R. D. (2020). Targeting the RNA Polymerase I Transcription for Cancer Therapy Comes of Age. Cells, 9(2). https://doi.org/10.3390/cells9020266 Published in: Cells Document Version: Publisher's PDF, also known as Version of record Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights © 2020 The Authors. This is an open access article published under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the Research Portal that you believe breaches copyright or violates any law, please contact [email protected]. Download date:26. Sep. 2021 cells Review Targeting the RNA Polymerase I Transcription for Cancer Therapy Comes of Age Rita Ferreira 1,* , John S.