Research articles for Molecular Biology BIOL5304 project 2009

This list will be updated periodically.

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Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation.
Fabian MR, Mathonnet G, Sundermeier T, Mathys H, Zipprich JT, Svitkin YV, Rivas F, Jinek M, Wohlschlegel J, Doudna JA, Chen CY, Shyu AB, Yates JR 3rd, Hannon GJ, Filipowicz W, Duchaine TF, Sonenberg N.
Mol Cell. 2009 Sep 25;35(6):868-80

Drosophila miR2 primarily targets the m7GpppN cap structure for translational repression.
Zdanowicz A, Thermann R, Kowalska J, Jemielity J, Duncan K, Preiss T, Darzynkiewicz E, Hentze MW.
Mol Cell. 2009 Sep 25;35(6):881-8.

EF-G2mt is an exclusive recycling factor in mammalian mitochondrial protein synthesis.
Tsuboi M, Morita H, Nozaki Y, Akama K, Ueda T, Ito K, Nierhaus KH, Takeuchi N.
Mol Cell. 2009 Aug 28;35(4):502-10.

Trypanosomes have six mitochondrial DNA helicases with one controlling kinetoplast maxicircle replication.
Liu B, Wang J, Yaffe N, Lindsay ME, Zhao Z, Zick A, Shlomai J, Englund PT.
Mol Cell. 2009 Aug 28;35(4):490-501

yFACT induces global accessibility of nucleosomal DNA without H2A-H2B displacement.
Xin H, Takahata S, Blanksma M, McCullough L, Stillman DJ, Formosa T.
Mol Cell. 2009 Aug 14;35(3):365-76.

SOSS complexes participate in the maintenance of genomic stability.
Huang J, Gong Z, Ghosal G, Chen J.
Mol Cell. 2009 Aug 14;35(3):384-93

Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
Sydow JF, Brueckner F, Cheung AC, Damsma GE, Dengl S, Lehmann E, Vassylyev D, Cramer P.
Mol Cell. 2009 Jun 26;34(6):710-21.

Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae.
Azvolinsky A, Giresi PG, Lieb JD, Zakian VA.
Mol Cell. 2009 Jun 26;34(6):722-34.

The ordered transcription of RNA domains is not essential for ribosome biogenesis in Escherichia coli.
Kitahara K, Suzuki T.
Mol Cell. 2009 Jun 26;34(6):760-6.

Potent transcriptional interference by pausing of RNA polymerases over a downstream promoter.
Palmer AC, Ahlgren-Berg A, Egan JB, Dodd IB, Shearwin KE.
Mol Cell. 2009 Jun 12;34(5):545-55.

Polypyrimidine tract binding protein stabilizes the encephalomyocarditis virus IRES structure via binding multiple sites in a unique orientation.
Kafasla P, Morgner N, Pöyry TA, Curry S, Robinson CV, Jackson RJ.
Mol Cell. 2009 Jun 12;34(5):556-68.

Resetting the site: redirecting integration of an insertion sequence in a predictable way.
Guynet C, Achard A, Hoang BT, Barabas O, Hickman AB, Dyda F, Chandler M.
Mol Cell. 2009 Jun 12;34(5):612-9.

FACT and Asf1 regulate nucleosome dynamics and coactivator binding at the HO promoter.
Takahata S, Yu Y, Stillman DJ.
Mol Cell. 2009 May 14;34(4):405-15

Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the transition from serine 5 to serine 2 phosphorylation.
Mosley AL, Pattenden SG, Carey M, Venkatesh S, Gilmore JM, Florens L, Workman JL, Washburn MP.
Mol Cell. 2009 Apr 24;34(2):168-78

The plasticity of a translation arrest motif yields insights into nascent polypeptide recognition inside the ribosome tunnel.
Yap MN, Bernstein HD.
Mol Cell. 2009 Apr 24;34(2):201-11.

Regulated proteolysis of DNA polymerase eta during the DNA-damage response in C. elegans.
Kim SH, Michael WM.
Mol Cell. 2008 Dec 26;32(6):757-66.

Gaur R, Grasso D, Datta PP, Krishna PD, Das G, Spencer A, Agrawal RK, Spremulli L, Varshney U.
A single mammalian mitochondrial translation initiation factor functionally replaces two bacterial factors.
Mol Cell. 2008 Feb 1;29(2):180-90.

Organization of an activator-bound RNA polymerase holoenzyme.
Bose D, Pape T, Burrows PC, Rappas M, Wigneshweraraj SR, Buck M, Zhang X.
Mol Cell. 2008 Nov 7;32(3):337-46.

Guide RNA-binding complex from mitochondria of trypanosomatids.
Weng J, Aphasizheva I, Etheridge RD, Huang L, Wang X, Falick AM, Aphasizhev R.
Mol Cell. 2008 Oct 24;32(2):198-209.

Polyadenylation linked to transcription termination directs the processing of snoRNA precursors in yeast.
Grzechnik P, Kufel J.
Mol Cell. 2008 Oct 24;32(2):247-58

DNA Recognition and Wrapping by Escherichia coli RcnR.
Iwig JS, Chivers PT.
J Mol Biol. 2009 Aug 21

Archaeal aIF2B interacts with eukaryotic translation initiation factors eIF2alpha and eIF2Balpha: Implications for aIF2B function and eIF2B regulation.
Dev K, Santangelo TJ, Rothenburg S, Neculai D, Dey M, Sicheri F, Dever TE, Reeve JN, Hinnebusch AG.
J Mol Biol. 2009 Sep 25;392(3):701-22

Amino acid architecture that influences dNTP insertion efficiency in Y-family DNA polymerase V of E. coli.
Seo KY, Yin J, Donthamsetti P, Chandani S, Lee CH, Loechler EL.
J Mol Biol. 2009 Sep 18;392(2):270-82

ATP binding and hydrolysis by Mcm2 regulate DNA binding by Mcm complexes.
Stead BE, Sorbara CD, Brandl CJ, Davey MJ.
J Mol Biol. 2009 Aug 14;391(2):301-13

Two structurally independent domains of E. coli NusG create regulatory plasticity via distinct interactions with RNA polymerase and regulators.
Mooney RA, Schweimer K, Rösch P, Gottesman M, Landick R.
J Mol Biol. 2009 Aug 14;391(2):341-58

Chromatin remodelers act globally, sequence positions nucleosomes locally.
Partensky PD, Narlikar GJ.
J Mol Biol. 2009 Aug 7;391(1):12-25.

Internal regulatory interactions determine DNA binding specificity by a Hox transcription factor.
Liu Y, Matthews KS, Bondos SE.
J Mol Biol. 2009 Jul 24;390(4):760-74.

Analysis of four-way junctions in RNA structures.
Laing C, Schlick T.
J Mol Biol. 2009 Jul 17;390(3):547-59.

Dynamic regulatory interactions of rad51, rad52, and replication protein-a in recombination intermediates.
Sugiyama T, Kantake N.
J Mol Biol. 2009 Jul 3;390(1):45-55

Topologies of complexes containing O6-alkylguanine-DNA alkyltransferase and DNA.
Adams CA, Melikishvili M, Rodgers DW, Rasimas JJ, Pegg AE, Fried MG.
J Mol Biol. 2009 Jun 5;389(2):248-63

Mechanism of ATP-driven PCNA clamp loading by S. cerevisiae RFC.
Chen S, Levin MK, Sakato M, Zhou Y, Hingorani MM.
J Mol Biol. 2009 May 8;388(3):431-42

The structure of Sox17 bound to DNA reveals a conserved bending topology but selective protein interaction platforms.
Palasingam P, Jauch R, Ng CK, Kolatkar PR.
J Mol Biol. 2009 May 8;388(3):619-30

The genome of Bacillus subtilis bacteriophage SPO1.
Stewart CR, Casjens SR, Cresawn SG, Houtz JM, Smith AL, Ford ME, Peebles CL, Hatfull GF, Hendrix RW, Huang WM, Pedulla ML.
J Mol Biol. 2009 Apr 24;388(1):48-70

Hormonal regulation of the E75 gene in Drosophila: identifying functional regulatory elements through computational and biological analysis.
Bernardo TJ, Dubrovskaya VA, Jannat H, Maughan B, Dubrovsky EB.
J Mol Biol. 2009 Apr 10;387(4):794-808

Conserved element of the dicistrovirus IGR IRES that mimics an E-site tRNA/ribosome interaction mediates multiple functions.
Jang CJ, Lo MC, Jan E.
J Mol Biol. 2009 Mar 20;387(1):42-58.

Sliding clamp-DNA interactions are required for viability and contribute to DNA polymerase management in Escherichia coli.
Heltzel JM, Scouten Ponticelli SK, Sanders LH, Duzen JM, Cody V, Pace J, Snell EH, Sutton MD.
J Mol Biol. 2009 Mar 20;387(1):74-91

Understanding the sequence specificity of tRNA binding to elongation factor Tu using tRNA mutagenesis.
Schrader JM, Chapman SJ, Uhlenbeck OC.
J Mol Biol. 2009 Mar 13;386(5):1255-64.

Recycling of aborted ribosomal 50S subunit-nascent chain-tRNA complexes by the heat shock protein Hsp15.
Jiang L, Schaffitzel C, Bingel-Erlenmeyer R, Ban N, Korber P, Koning RI, de Geus DC, Plaisier JR, Abrahams JP.
J Mol Biol. 2009 Mar 13;386(5):1357-67

Transcript elongation factor TFIIS is involved in arabidopsis seed dormancy.
Grasser M, Kane CM, Merkle T, Melzer M, Emmersen J, Grasser KD.
J Mol Biol. 2009 Feb 27;386(3):598-611.

Identification of the SSB binding site on E. coli RecQ reveals a conserved surface for binding SSB's C terminus.
Shereda RD, Reiter NJ, Butcher SE, Keck JL.
J Mol Biol. 2009 Feb 27;386(3):612-25.

Effects of CpG methylation on recognition of DNA by the tumour suppressor p53.
Petrovich M, Veprintsev DB.
J Mol Biol. 2009 Feb 13;386(1):72-80

How do type II topoisomerases use ATP hydrolysis to simplify DNA topology beyond equilibrium? Investigating the relaxation reaction of nonsupercoiling type II topoisomerases.
Stuchinskaya T, Mitchenall LA, Schoeffler AJ, Corbett KD, Berger JM, Bates AD, Maxwell A.
J Mol Biol. 2009 Feb 6;385(5):1397-408

Specificity of pyrrolysyl-tRNA synthetase for pyrrolysine and pyrrolysine analogs.
Li WT, Mahapatra A, Longstaff DG, Bechtel J, Zhao G, Kang PT, Chan MK, Krzycki JA.
J Mol Biol. 2009 Jan 30;385(4):1156-64

The ribosomal grip of the peptidyl-tRNA is critical for reading frame maintenance.
Näsvall SJ, Nilsson K, Björk GR.
J Mol Biol. 2009 Jan 16;385(2):350-67

A DExH/D-box protein coordinates the two steps of splicing in a group I intron.
Bifano AL, Caprara MG.
J Mol Biol. 2008 Nov 14;383(3):667-82

• Asuteka Nagao, Takeo Suzuki, Takayuki Katoh, Yuriko Sakaguchi, and Tsutomu Suzuki
Biogenesis of glutaminyl-mt tRNAGln in human mitochondria
PNAS 2009 106:16209-16214; published online before print September 9, 2009, doi:10.1073/pnas.0907602106

Redox signaling between DNA repair proteins for efficient lesion detection.
Boal AK, Genereux JC, Sontz PA, Gralnick JA, Newman DK, Barton JK.
Proc Natl Acad Sci U S A. 2009 Aug 31

Rho directs widespread termination of intragenic and stable RNA transcription.
Peters JM, Mooney RA, Kuan PF, Rowland JL, Keles S, Landick R.
Proc Natl Acad Sci U S A. 2009 Aug 20

Biochemical basis for the essential genetic requirements of RecA and the {beta}-clamp in Pol V activation.
Fujii S, Fuchs RP.
Proc Natl Acad Sci U S A. 2009 Aug 19

Phosphorylation of the RNA polymerase II C-terminal domain by TFIIH kinase is not essential for transcription of Saccharomyces cerevisiae genome.
Hong SW, Hong SM, Yoo JW, Lee YC, Kim S, Lis JT, Lee DK.
Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14276-80

Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB.
Yu B, Hunt JF.
Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14315-20

The BRC repeats of human BRCA2 differentially regulate RAD51 binding on single- versus double-stranded DNA to stimulate strand exchange.
Shivji MK, Mukund SR, Rajendra E, Chen S, Short JM, Savill J, Klenerman D, Venkitaraman AR.
Proc Natl Acad Sci U S A. 2009 Aug 11;106(32):13254-9.

Cysteine modification of a specific repressor protein controls the translational status of nucleus-encoded LHCII mRNAs in Chlamydomonas.
Wobbe L, Blifernez O, Schwarz C, Mussgnug JH, Nickelsen J, Kruse O.
Proc Natl Acad Sci U S A. 2009 Aug 11;106(32):13290-5

A model for DNA polymerase switching involving a single cleft and the rim of the sliding clamp.
Heltzel JM, Maul RW, Scouten Ponticelli SK, Sutton MD.
Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12664-9

DNA wrapping is required for DNA damage recognition in the Escherichia coli DNA nucleotide excision repair pathway.
Wang H, Lu M, Tang MS, Van Houten B, Ross JB, Weinfeld M, Le XC.
Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12849-54.

Protein-free small nuclear RNAs catalyze a two-step splicing reaction.
Valadkhan S, Mohammadi A, Jaladat Y, Geisler S.
Proc Natl Acad Sci U S A. 2009 Jul 21;106(29):11901-6.

Nej1 recruits the Srs2 helicase to DNA double-strand breaks and supports repair by a single-strand annealing-like mechanism.
Carter SD, Vigasová D, Chen J, Chovanec M, Aström SU.
Proc Natl Acad Sci U S A. 2009 Jul 21;106(29):12037-42

The glucanosyltransferase Gas1 functions in transcriptional silencing.
Koch MR, Pillus L.
Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11224-9.

Direct functional interaction of initiation factor eIF4G with type 1 internal ribosomal entry sites.
de Breyne S, Yu Y, Unbehaun A, Pestova TV, Hellen CU.
Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9197-202

The protein factors MBNL1 and U2AF65 bind alternative RNA structures to regulate splicing.
Warf MB, Diegel JV, von Hippel PH, Berglund JA.
Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9203-8.

Mechanism of sequence-specific pausing of bacterial RNA polymerase.
Kireeva ML, Kashlev M.
Proc Natl Acad Sci U S A. 2009 Jun 2;106(22):8900-5

Translesion DNA polymerases remodel the replisome and alter the speed of the replicative helicase.
Indiani C, Langston LD, Yurieva O, Goodman MF, O'Donnell M.
Proc Natl Acad Sci U S A. 2009 Apr 14;106(15):6031-8.

B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes.
Yakovchuk P, Goodrich JA, Kugel JF.
Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5569-74.

Synthesis of programmable integrases.
Gordley RM, Gersbach CA, Barbas CF 3rd.
Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5053-8.

Distinct modes of gene regulation by a cell-specific transcriptional activator.
Sengupta T, Cohet N, Morlé F, Bieker JJ.
Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4213-8

Sigma factor mimicry involved in regulation of general stress response.
Francez-Charlot A, Frunzke J, Reichen C, Ebneter JZ, Gourion B, Vorholt JA.
Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3467-72.

Drosophila hnRNP A1 homologs Hrp36/Hrp38 enhance U2-type versus U12-type splicing to regulate alternative splicing of the prospero twintron.
Borah S, Wong AC, Steitz JA.
Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2577-82

Splice-site pairing is an intrinsically high fidelity process.
Fox-Walsh KL, Hertel KJ.
Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1766-71.

The promoter spacer influences transcription initiation via sigma70 region 1.1 of Escherichia coli RNA polymerase.
Hook-Barnard IG, Hinton DM.
Proc Natl Acad Sci U S A. 2009 Jan 20;106(3):737-42.

Esnault C, Ghavi-Helm Y, Brun S, Soutourina J, Van Berkum N, Boschiero C, Holstege F, Werner M.
Mediator-dependent recruitment of TFIIH modules in preinitiation complex.
Mol Cell. 2008 Aug 8;31(3):337-46.

Lutzmann M, Méchali M.
MCM9 binds Cdt1 and is required for the assembly of prereplication complexes.
Mol Cell. 2008 Jul 25;31(2):190-200.

Kuehner JN, Brow DA.
Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation.
Mol Cell. 2008 Jul 25;31(2):201-11. see comment

Coin F, Oksenych V, Mocquet V, Groh S, Blattner C, Egly JM.
Nucleotide excision repair driven by the dissociation of CAK from TFIIH.
Mol Cell. 2008 Jul 11;31(1):9-20.

Kaplan CD, Larsson KM, Kornberg RD.
The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin.
Mol Cell. 2008 Jun 6;30(5):547-56.

Ørom UA, Nielsen FC, Lund AH.
MicroRNA-10a binds the 5'UTR of ribosomal protein mRNAs and enhances their translation.
Mol Cell. 2008 May 23;30(4):460-71.

Dai L, Chai D, Gu SQ, Gabel J, Noskov SY, Blocker FJ, Lambowitz AM, Zimmerly S.
A three-dimensional model of a group II intron RNA and its interaction with the intron-encoded reverse transcriptase.
Mol Cell. 2008 May 23;30(4):472-85.

Nick McElhinny SA, Gordenin DA, Stith CM, Burgers PM, Kunkel TA.
Division of labor at the eukaryotic replication fork.
Mol Cell. 2008 Apr 25;30(2):137-44. see commentary

Mouw KW, Rowland SJ, Gajjar MM, Boocock MR, Stark WM, Rice PA.
Architecture of a serine recombinase-DNA regulatory complex.
Mol Cell. 2008 Apr 25;30(2):145-55.

Wang JX, Lee ER, Morales DR, Lim J, Breaker RR.
Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling.
Mol Cell. 2008 Mar 28;29(6):691-702.

West S, Proudfoot NJ, Dye MJ.
Molecular dissection of mammalian RNA polymerase II transcriptional termination.
Mol Cell. 2008 Mar 14;29(5):600-10.

Kyriacou SV, Deutscher MP.
An important role for the multienzyme aminoacyl-tRNA synthetase complex in mammalian translation and cell growth.
Mol Cell. 2008 Feb 29;29(4):419-27. Erratum in: Mol Cell. 2008 Mar 28;29(6):793-5.

Deshmukh MV, Jones BN, Quang-Dang DU, Flinders J, Floor SN, Kim C, Jemielity J, Kalek M, Darzynkiewicz E, Gross JD.
mRNA decapping is promoted by an RNA-binding channel in Dcp2.
Mol Cell. 2008 Feb 15;29(3):324-36.

Berlatzky IA, Rouvinski A, Ben-Yehuda S.
Spatial organization of a replicating bacterial chromosome.
Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):14136-40. Epub 2008 Sep 8

Schweidenback CT, Baker TA.
Dissecting the roles of MuB in Mu transposition: ATP regulation of DNA binding is not essential for target delivery.
Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12101-7. Epub 2008 Aug 21.

Levy A, Eyal M, Hershkovits G, Salmon-Divon M, Klutstein M, Katcoff DJ.
Yeast linker histone Hho1p is required for efficient RNA polymerase I processivity and transcriptional silencing at the ribosomal DNA.
Proc Natl Acad Sci U S A. 2008 Aug 19;105(33):11703-8. Epub 2008 Aug 7.

Argueso JL, Westmoreland J, Mieczkowski PA, Gawel M, Petes TD, Resnick MA.
Double-strand breaks associated with repetitive DNA can reshape the genome.
Proc Natl Acad Sci U S A. 2008 Aug 19;105(33):11845-50. Epub 2008 Aug 13.

Di Giacco V, Márquez V, Qin Y, Pech M, Triana-Alonso FJ, Wilson DN, Nierhaus KH.
Shine-Dalgarno interaction prevents incorporation of noncognate amino acids at the codon following the AUG.
Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10715-20. Epub 2008 Jul 30.

Voineagu I, Narayanan V, Lobachev KS, Mirkin SM.
Replication stalling at unstable inverted repeats: interplay between DNA hairpins and fork stabilizing proteins.
Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):9936-41. Epub 2008 Jul 15.

Ivanov IP, Loughran G, Atkins JF.
uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs.
Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):10079-84. Epub 2008 Jul 14.

Kong YW, Cannell IG, de Moor CH, Hill K, Garside PG, Hamilton TL, Meijer HA, Dobbyn HC, Stoneley M, Spriggs KA, Willis AE, Bushell M.
The mechanism of micro-RNA-mediated translation repression is determined by the promoter of the target gene.
Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):8866-71. Epub 2008 Jun 25

Routh A, Sandin S, Rhodes D.
Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure.
Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):8872-7. Epub 2008 Jun 26

Stuwe T, Hothorn M, Lejeune E, Rybin V, Bortfeld M, Scheffzek K, Ladurner AG.
The FACT Spt16 "peptidase" domain is a histone H3-H4 binding module.
Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):8884-9. Epub 2008 Jun 25

Smith ER, Winter B, Eissenberg JC, Shilatifard A.
Regulation of the transcriptional activity of poised RNA polymerase II by the elongation factor ELL.
Proc Natl Acad Sci U S A. 2008 Jun 24;105(25):8575-9. Epub 2008 Jun 17.

Hendrix DA, Hong JW, Zeitlinger J, Rokhsar DS, Levine MS.
Promoter elements associated with RNA Pol II stalling in the Drosophila embryo.
Proc Natl Acad Sci U S A. 2008 Jun 3;105(22):7762-7. Epub 2008 May 27.

Gegonne A, Weissman JD, Lu H, Zhou M, Dasgupta A, Ribble R, Brady JN, Singer DS.
TFIID component TAF7 functionally interacts with both TFIIH and P-TEFb.
Proc Natl Acad Sci U S A. 2008 Apr 8;105(14):5367-72. Epub 2008 Apr 7

Collier J, McAdams HH, Shapiro L.
A DNA methylation ratchet governs progression through a bacterial cell cycle.
Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):17111-6. Epub 2007 Oct 17

Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, Lander ES.
Distinguishing protein-coding and noncoding genes in the human genome.
Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19428-33. Epub 2007 Nov 26

Sevostyanova A, Svetlov V, Vassylyev DG, Artsimovitch I.
The elongation factor RfaH and the initiation factor sigma bind to the same site on the transcription elongation complex.
Proc Natl Acad Sci U S A. 2008 Jan 22;105(3):865-70. Epub 2008 Jan 14.

Simon SM, Sousa FJ, Mohana-Borges R, Walker GC.
Regulation of Escherichia coli SOS mutagenesis by dimeric intrinsically disordered umuD gene products.
Proc Natl Acad Sci U S A. 2008 Jan 29;105(4):1152-7. Epub 2008 Jan 23

Haugen SP, Ross W, Manrique M, Gourse RL.
Fine structure of the promoter-sigma region 1.2 interaction.
Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3292-7. Epub 2008 Feb 19

Hatoum A, Roberts J.
Prevalence of RNA polymerase stalling at Escherichia coli promoters after open complex formation.
Mol Microbiol. 2008 Apr;68(1):17-28.

Zawilak-Pawlik A, Kois A, Stingl K, Boneca IG, Skrobuk P, Piotr J, Lurz R, Zakrzewska-Czerwi?ska J, Labigne A.
HobA--a novel protein involved in initiation of chromosomal replication in Helicobacter pylori.
Mol Microbiol. 2007 Aug;65(4):979-94

Maul RW, Ponticelli SK, Duzen JM, Sutton MD.
Differential binding of Escherichia coli DNA polymerases to the beta-sliding clamp.
Mol Microbiol. 2007 Aug;65(3):811-27

Semsey S, Krishna S, Sneppen K, Adhya S.
Signal integration in the galactose network of Escherichia coli.
Mol Microbiol. 2007 Jul;65(2):465-76.

Bichara M, Pinet I, Lambert IB, Fuchs RP.
RecA-mediated excision repair: a novel mechanism for repairing DNA lesions at sites of arrested DNA synthesis.
Mol Microbiol. 2007 Jul;65(1):218-29.

Loughman JA, Caparon MG.
Comparative functional analysis of the lac operons in Streptococcus pyogenes.
Mol Microbiol. 2007 Apr;64(2):269-80

Hendrickson H, Lawrence JG.
Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites.
Mol Microbiol. 2007 Apr;64(1):42-56

Checa SK, Espariz M, Audero ME, Botta PE, Spinelli SV, Soncini FC.
Bacterial sensing of and resistance to gold salts.
Mol Microbiol. 2007 Mar;63(5):1307-18

Deighan P, Hochschild A.
The bacteriophage lambdaQ anti-terminator protein regulates late gene expression as a stable component of the transcription elongation complex.
Mol Microbiol. 2007 Feb;63(3):911-20.

Longstaff DG, Blight SK, Zhang L, Green-Church KB, Krzycki JA.
In vivo contextual requirements for UAG translation as pyrrolysine.
Mol Microbiol. 2007 Jan;63(1):229-41.

Caldara M, Minh PN, Bostoen S, Massant J, Charlier D.
ArgR-dependent Repression of Arginine and Histidine Transport Genes in Escherichia coli K-12.
J Mol Biol. 2007 Oct 19;373(2):251-67. Epub 2007 Aug 21.

Meslet-Cladiere L, Norais C, Kuhn J, Briffotaux J, Sloostra JW, Ferrari E, Hubscher U, Flament D, Myllykallio H.
A novel proteomic approach identifies new interaction partners for proliferating cell nuclear antigen.
J Mol Biol. 2007 Oct 5;372(5):1137-48. Epub 2007 Jun 27.

Ghosal G, Muniyappa K.
The Characterization of Saccharomyces cerevisiae Mre11/Rad50/Xrs2 Complex Reveals that Rad50 Negatively Regulates Mre11 Endonucleolytic but not the Exonucleolytic Activity.
J Mol Biol. 2007 Sep 28;372(4):864-82. Epub 2007 Jul 21.

Fujii S, Fuchs RP.
Interplay among replicative and specialized DNA polymerases determines failure or success of translesion synthesis pathways.
J Mol Biol. 2007 Sep 28;372(4):883-93. Epub 2007 Aug 2.

Patikoglou GA, Westblade LF, Campbell EA, Lamour V, Lane WJ, Darst SA.
Crystal Structure of the Escherichia coli Regulator of sigma(70), Rsd, in Complex with sigma(70) Domain 4.
J Mol Biol. 2007 Sep 21;372(3):649-59. Epub 2007 Jul 3.

Chalissery J, Banerjee S, Bandey I, Sen R.
Transcription termination defective mutants of Rho: role of different functions of Rho in releasing RNA from the elongation complex.
J Mol Biol. 2007 Aug 24;371(4):855-72. Epub 2007 Jun 9.

Fernandez AG, Anderson JN.
Nucleosome positioning determinants.
J Mol Biol. 2007 Aug 17;371(3):649-68. Epub 2007 Jun 4.

Tolstorukov MY, Colasanti AV, McCandlish DM, Olson WK, Zhurkin VB.
A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning.
J Mol Biol. 2007 Aug 17;371(3):725-38. Epub 2007 May 24.

Zhang W, Dillingham MS, Thomas CD, Allen S, Roberts CJ, Soultanas P.
Directional loading and stimulation of PcrA helicase by the replication initiator protein RepD.
J Mol Biol. 2007 Aug 10;371(2):336-48. Epub 2007 May 24.

Two papers together:
Murphy KC.
The lambda Gam protein inhibits RecBCD binding to dsDNA ends.
J Mol Biol. 2007 Aug 3;371(1):19-24. Epub 2007 Jun 2.
Court R, Cook N, Saikrishnan K, Wigley D.
The crystal structure of lambda-Gam protein suggests a model for RecBCD inhibition.
J Mol Biol. 2007 Aug 3;371(1):25-33. Epub 2007 May 18.

Tanaka A, Takano Y, Ohnishi Y, Horinouchi S.
AfsR recruits RNA polymerase to the afsS promoter: a model for transcriptional activation by SARPs.
J Mol Biol. 2007 Jun 1;369(2):322-33

Sanderson LE, Uhlenbeck OC.
Directed mutagenesis identifies amino acid residues involved in elongation factor Tu binding to yeast Phe-tRNAPhe.
J Mol Biol. 2007 Apr 20;368(1):119-30.

Liu C, Gamper H, Shtivelband S, Hauenstein S, Perona JJ, Hou YM.
Kinetic quality control of anticodon recognition by a eukaryotic aminoacyl-tRNA synthetase.
J Mol Biol. 2007 Apr 6;367(4):1063-78

Slocum SL, Buss JA, Kimura Y, Bianco PR.
Characterization of the ATPase activity of the Escherichia coli RecG protein reveals that the preferred cofactor is negatively supercoiled DNA.
J Mol Biol. 2007 Mar 30;367(3):647-64

Nawaz MH, Pang YL, Martinis SA.
Molecular and functional dissection of a putative RNA-binding region in yeast mitochondrial leucyl-tRNA synthetase.
J Mol Biol. 2007 Mar 23;367(2):384-94

Hede MS, Petersen RL, Frohlich RF, Kruger D, Andersen FF, Andersen AH, Knudsen BR.
Resolution of Holliday junction substrates by human topoisomerase I.Hede MS, Petersen RL, Frohlich RF, Kruger D, Andersen FF, Andersen AH, Knudsen BR.
J Mol Biol. 2007 Jan 26;365(4):1076-92

Xu F, Zhang Q, Zhang K, Xie W, Grunstein M.
Sir2 Deacetylates Histone H3 Lysine 56 to Regulate Telomeric Heterochromatin Structure in Yeast.
Mol Cell. 2007 Sep 21;27(6):890-900.

Soleimanpour-Lichaei HR, Kuhl I, Gaisne M, Passos JF, Wydro M, Rorbach J, Temperley R, Bonnefoy N, Tate W, Lightowlers R, Chrzanowska-Lightowlers Z.
mtRF1a is a human mitochondrial translation release factor decoding the major termination codons UAA and UAG.
Mol Cell. 2007 Sep 7;27(5):745-57.

Singh G, Jakob S, Kleedehn MG, Lykke-Andersen J.
Communication with the exon-junction complex and activation of nonsense-mediated decay by human Upf proteins occur in the cytoplasm.
Mol Cell. 2007 Sep 7;27(5):780-92.

Prasad R, Liu Y, Deterding LJ, Poltoratsky VP, Kedar PS, Horton JK, Kanno S, Asagoshi K, Hou EW, Khodyreva SN, Lavrik OI, Tomer KB, Yasui A, Wilson SH.
HMGB1 is a cofactor in mammalian base excision repair.
Mol Cell. 2007 Sep 7;27(5):829-41.

Zhang H, Freudenreich CH.
An AT-rich sequence in human common fragile site FRA16D causes fork stalling and chromosome breakage in S. cerevisiae.
Mol Cell. 2007 Aug 3;27(3):367-79.

Jeronimo C, Forget D, Bouchard A, Li Q, Chua G, Poitras C, Therien C, Bergeron D, Bourassa S, Greenblatt J, Chabot B, Poirier GG, Hughes TR, Blanchette M, Price DH, Coulombe B.
Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme.
Mol Cell. 2007 Jul 20;27(2):262-74.

Lopper M, Boonsombat R, Sandler SJ, Keck JL.
A hand-off mechanism for primosome assembly in replication restart.
Mol Cell. 2007 Jun 22;26(6):781-93.

Bae NS, Baumann P.
A RAP1/TRF2 complex inhibits nonhomologous end-joining at human telomeric DNA ends.
Mol Cell. 2007 May 11;26(3):323-34.

Tomko EJ, Fischer CJ, Niedziela-Majka A, Lohman TM.
A nonuniform stepping mechanism for E. coli UvrD monomer translocation along single-stranded DNA.
Mol Cell. 2007 May 11;26(3):335-47

Yao W, Roser D, Kohler A, Bradatsch B, Bassler J, Hurt E.
Nuclear export of ribosomal 60S subunits by the general mRNA export receptor Mex67-Mtr2.
Mol Cell. 2007 Apr 13;26(1):51-62.

Bai Y, Auperin TC, Chou CY, Chang GG, Manley JL, Tong L.
Crystal structure of murine CstF-77: dimeric association and implications for polyadenylation of mRNA precursors.
Mol Cell. 2007 Mar 23;25(6):863-75.

Jamai A, Imoberdorf RM, Strubin M.
Continuous histone H2B and transcription-dependent histone H3 exchange in yeast cells outside of replication.
Mol Cell. 2007 Feb 9;25(3):345-55.

Donmez G, Hartmuth K, Kastner B, Will CL, Luhrmann R.
The 5' end of U2 snRNA is in close proximity to U1 and functional sites of the pre-mRNA in early spliceosomal complexes.
Mol Cell. 2007 Feb 9;25(3):399-411.

Govind CK, Zhang F, Qiu H, Hofmeyer K, Hinnebusch AG.
Gcn5 promotes acetylation, eviction, and methylation of nucleosomes in transcribed coding regions.
Mol Cell. 2007 Jan 12;25(1):31-42.

Wu J, Zhang S, Meng Q, Cao H, Li Z, Li X, Shi S, Kim DH, Bi L, Turro NJ, Ju J.
3'-O-modified nucleotides as reversible terminators for pyrosequencing.
Proc Natl Acad Sci U S A. 2007 Oct 16;104(42):16462-7. Epub 2007 Oct 8.

Guglielmi B, Soutourina J, Esnault C, Werner M.
TFIIS elongation factor and Mediator act in conjunction during transcription initiation in vivo.
Proc Natl Acad Sci U S A. 2007 Oct 9;104(41):16062-7. Epub 2007 Sep 27.

Martin V, Du LL, Rozenzhak S, Russell P.
Protection of telomeres by a conserved Stn1-Ten1 complex.
Proc Natl Acad Sci U S A. 2007 Aug 28;104(35):14038-43. Epub 2007 Aug 22.

Pluciennik A, Modrich P.
Protein roadblocks and helix discontinuities are barriers to the initiation of mismatch repair.
Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12709-13. Epub 2007 Jul 9.

Alic N, Ayoub N, Landrieux E, Favry E, Baudouin-Cornu P, Riva M, Carles C.
Selectivity and proofreading both contribute significantly to the fidelity of RNA polymerase III transcription.
Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10400-5. Epub 2007 Jun 6.

Saldi T, Wilusz C, MacMorris M, Blumenthal T.
Functional redundancy of worm spliceosomal proteins U1A and U2B''.
Proc Natl Acad Sci U S A. 2007 Jun 5;104(23):9753-7. Epub 2007 May 29.

Romi E, Baran N, Gantman M, Shmoish M, Min B, Collins K, Manor H.
High-resolution physical and functional mapping of the template adjacent DNA binding site in catalytically active telomerase.
Proc Natl Acad Sci U S A. 2007 May 22;104(21):8791-6. Epub 2007 May 9.

Zhang H, Reese JC.
Exposing the core promoter is sufficient to activate transcription and alter coactivator requirement at RNR3.
Proc Natl Acad Sci U S A. 2007 May 22;104(21):8833-8. Epub 2007 May 14.

Rubio MA, Pastar I, Gaston KW, Ragone FL, Janzen CJ, Cross GA, Papavasiliou FN, Alfonzo JD.
An adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U deamination of DNA.
Proc Natl Acad Sci U S A. 2007 May 8;104(19):7821-6. Epub 2007 May 1.

Huang Y, Greene E, Murray Stewart T, Goodwin AC, Baylin SB, Woster PM, Casero RA Jr.
Inhibition of lysine-specific demethylase 1 by polyamine analogues results in reexpression of aberrantly silenced genes.
Proc Natl Acad Sci U S A. 2007 May 8;104(19):8023-8. Epub 2007 Apr 26.

Last updated Saturday, November 21, 2009

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Copyright 2009, Steven B. Vik, Southern Methodist University