PUB - Publikationen an der Universität Bielefeld

THUMP – a predicted RNA-binding domain shared by 4-thiouridine, pseudouridine synthases and RNA methylases
Aravind L, Koonin EV., 2001

Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening.
Aza-Blanc P, Cooper CL, Wagner K, Batalov S, Deveraux QL, Cooke MP., Mol. Cell 12(3), 2003
PMID: 14527409

Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM
Bates PA, Kelley LA, MacCallum RM, Sternberg MJE., 2001

The yeast gene YNL292w encodes a pseudouridine synthase (Pus4) catalyzing the formation of psi55 in both mitochondrial and cytoplasmic tRNAs.
Becker HF, Motorin Y, Planta RJ, Grosjean H., Nucleic Acids Res. 25(22), 1997
PMID: 9358157

Pseudouridine formation in archaeal RNAs: The case of Haloferax volcanii.
Blaby IK, Majumder M, Chatterjee K, Jana S, Grosjean H, de Crecy-Lagard V, Gupta R., RNA 17(7), 2011
PMID: 21628430

The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl
Bombarely A, Menda N, Tecle IY, Buels RM, Strickler S, Fischer-York T, Pujar A, Leto J, Gosselin J, Mueller LA., 2011

Enzymatic characterization and mutational studies of TruD--the fifth family of pseudouridine synthases.
Chan CM, Huang RH., Arch. Biochem. Biophys. 489(1-2), 2009
PMID: 19664587

Arabidopsis type I metacaspases control cell death.
Coll NS, Vercammen D, Smidler A, Clover C, Van Breusegem F, Dangl JL, Epple P., Science 330(6009), 2010
PMID: 21097903

16S ribosomal RNA pseudouridine synthase RsuA of Escherichia coli: deletion, mutation of the conserved Asp102 residue, and sequence comparison among all other pseudouridine synthases.
Conrad J, Niu L, Rudd K, Lane BG, Ofengand J., RNA 5(6), 1999
PMID: 10376875

The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I
Foster PG, Huang L, Santi DV, Stroud RM., 2000

SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling.
Guex N, Peitsch MC., Electrophoresis 18(15), 1997
PMID: 9504803

Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective
Guex N, Peitsch MC, Schwede T., 2009

Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA.
Gurha P, Gupta R., RNA 14(12), 2008
PMID: 18952823

The roles of the essential Asp-48 and highly conserved His-43 elucidated by the pH dependence of the pseudouridine synthase TruB.
Hamilton CS, Spedaliere CJ, Ginter JM, Johnston MV, Mueller EG., Arch. Biochem. Biophys. 433(1), 2005
PMID: 15581587

Pseudouridine synthases.
Hamma T, Ferre-D'Amare AR., Chem. Biol. 13(11), 2006
PMID: 17113994

Post-transcriptional nucleotide modification and alternative folding of RNA.
Helm M., Nucleic Acids Res. 34(2), 2006
PMID: 16452298

Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold.
Hoang C, Ferre-D'Amare AR., RNA 10(7), 2004
PMID: 15208439

Crystal Structure of Pseudouridine Synthase RluA: Indirect Sequence Readout through Protein-Induced RNA Structure
Hoang C, Chen J, Vizthum CA, Kandel JMS, Hamilton C, Mueller EG, Ferré-D’Amaré AR., 2006

Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme.
Hoang C, Ferre-D'Amare AR., Cell 107(7), 2001
PMID: 11779468

Searching protein structure databases with DaliLite v.3.
Holm L, Kaariainen S, Rosenstrom P, Schenkel A., Bioinformatics 24(23), 2008
PMID: 18818215

Dali server: conservation mapping in 3D.
Holm L, Rosenstrom P., Nucleic Acids Res. 38(Web Server issue), 2010
PMID: 20457744

Ensembl 2009.
Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Rios D, Schuster M, Slater G, Smedley D, Spooner W, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wilder S, Zadissa A, Birney E, Cunningham F, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Kasprzyk A, Proctor G, Smith J, Searle S, Flicek P., Nucleic Acids Res. 37(Database issue), 2008
PMID: 19033362

How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA.
Hur S, Stroud RM., Mol. Cell 26(2), 2007
PMID: 17466622

Reciprocal amplification of caspase-3 activity by nuclear export of a putative human RNA-modifying protein, PUS10 during TRAIL-induced apoptosis.
Jana S, Hsieh AC, Gupta R., Cell Death Dis 8(10), 2017
PMID: 28981101

An essential yeast protein, CBF5p, binds in vitro to centromeres and microtubules.
Jiang W, Middleton K, Yoon HJ, Fouquet C, Carbon J., Mol. Cell. Biol. 13(8), 1993
PMID: 8336724

Role of forefinger and thumb loops in production of Ψ54 and Ψ55 in tRNAs by archaeal Pus10.
Joardar A, Jana S, Fitzek E, Gurha P, Majumder M, Chatterjee K, Geisler M, Gupta R., RNA 19(9), 2013
PMID: 23898217

tRNA binding, positioning, and modification by the pseudouridine synthase Pus10.
Kamalampeta R, Keffer-Wilkes LC, Kothe U., J. Mol. Biol. 425(20), 2013
PMID: 23743107

A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya.
Kaya Y, Ofengand J., RNA 9(6), 2003
PMID: 12756329

The origin and early evolution of eukaryotes in the light of phylogenomics.
Koonin EV., Genome Biol. 11(5), 2010
PMID: 20441612

Constraints and plasticity in genome and molecular-phenome evolution
Koonin EV, Wolf YI., 2010

Clustal W and Clustal X version 2.0.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG., Bioinformatics 23(21), 2007
PMID: 17846036

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.
Letunic I, Bork P., Nucleic Acids Res. 39(Web Server issue), 2011
PMID: 21470960

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.
Letunic I, Bork P., Nucleic Acids Res. 44(W1), 2016
PMID: 27095192

Crystal structure of human Pus10, a novel pseudouridine synthase.
McCleverty CJ, Hornsby M, Spraggon G, Kreusch A., J. Mol. Biol. 373(5), 2007
PMID: 17900615

BLAST: at the core of a powerful and diverse set of sequence analysis tools.
McGinnis S, Madden TL., Nucleic Acids Res. 32(Web Server issue), 2004
PMID: 15215342

DNA and RNA Modification Enzymes
Mueller EG, Ferré-D’Amaré AR., 2009

Identification of the TRM2 gene encoding the tRNA(m5U54)methyltransferase of Saccharomyces cerevisiae.
Nordlund ME, Johansson JO, von Pawel-Rammingen U, Bystrom AS., RNA 6(6), 2000
PMID: 10864043

Purification, cloning, and properties of the tRNA psi 55 synthase from Escherichia coli.
Nurse K, Wrzesinski J, Bakin A, Lane BG, Ofengand J., RNA 1(1), 1995
PMID: 7489483

Cloning and restriction mapping of the trmA gene coding for transfer ribonucleic acid (5-methyluridine)-methyltransferase in Escherichia coli K-12.
Ny T, Bjork GR., J. Bacteriol. 142(2), 1980
PMID: 6247318

Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit
Pan H, Agarwalla S, Moustakas DT, Finer-Moore J, Stroud RM., 2003

DOBI is cleaved by caspases during TRAIL-induced apoptotic cell death.
Park SY, Shin JN, Woo HN, Piya S, Moon AR, Seo YW, Seol DW, Kim TH., BMB Rep 42(8), 2009
PMID: 19712588

Journey through the past: 150 million years of plant genome evolution.
Proost S, Pattyn P, Gerats T, Van de Peer Y., Plant J. 66(1), 2011
PMID: 21443623

Crystal structure of a Cbf5-Nop10-Gar1 complex and implications in RNA-guided pseudouridylation and dyskeratosis congenita.
Rashid R, Liang B, Baker DL, Youssef OA, He Y, Phipps K, Terns RM, Terns MP, Li H., Mol. Cell 21(2), 2006
PMID: 16427014

Role of ribothymidine in mammalian tRNAPhe.
Roe BA, Tsen HY., Proc. Natl. Acad. Sci. U.S.A. 74(9), 1977
PMID: 269424

Formation of the conserved pseudouridine at position 55 in archaeal tRNA.
Roovers M, Hale C, Tricot C, Terns MP, Terns RM, Grosjean H, Droogmans L., Nucleic Acids Res. 34(15), 2006
PMID: 16920741

Consequences of genome duplication.
Semon M, Wolfe KH., Curr. Opin. Genet. Dev. 17(6), 2007
PMID: 18006297

Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP.
Sivaraman J, Sauve V, Larocque R, Stura EA, Schrag JD, Cygler M, Matte A., Nat. Struct. Biol. 9(5), 2002
PMID: 11953756

Functional importance of motif I of pseudouridine synthases: mutagenesis of aligned lysine and proline residues.
Spedaliere CJ, Hamilton CS, Mueller EG., Biochemistry 39(31), 2000
PMID: 10924141

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.
Stamatakis A., Bioinformatics 22(21), 2006
PMID: 16928733

Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes.
Thomas BC, Pedersen B, Freeling M., Genome Res. 16(7), 2006
PMID: 16760422

Acquisition of a bacterial RumA-type tRNA(uracil-54, C5)-methyltransferase by Archaea through an ancient horizontal gene transfer.
Urbonavicius J, Auxilien S, Walbott H, Trachana K, Golinelli-Pimpaneau B, Brochier-Armanet C, Grosjean H., Mol. Microbiol. 67(2), 2007
PMID: 18069966

Type II metacaspases Atmc4 and Atmc9 of Arabidopsis thaliana cleave substrates after arginine and lysine.
Vercammen D, van de Cotte B, De Jaeger G, Eeckhout D, Casteels P, Vandepoele K, Vandenberghe I, Van Beeumen J, Inze D, Van Breusegem F., J. Biol. Chem. 279(44), 2004
PMID: 15326173

Are metacaspases caspases?
Vercammen D, Declercq W, Vandenabeele P, Van Breusegem F., J. Cell Biol. 179(3), 2007
PMID: 17967946

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach.
Whelan S, Goldman N., Mol. Biol. Evol. 18(5), 2001
PMID: 11319253

Mutations in SUPPRESSOR OF VARIEGATION1, a Factor Required for Normal Chloroplast Translation, Suppress var2-Mediated Leaf Variegation in Arabidopsis
Yu F, Liu X, Alsheikh M, Park S, Rodermel S., 2008