Limitation of ribosomal protein L11 availability in vivo affects translation termination.

Abstract:

:Historically referred to as "the GTPase center", the L11 binding region (L11BR) of Escherichia coli 23 S rRNA is a highly conserved structure that has been implicated in several essential functions during protein synthesis. Here, in vivo expression of an RNA fragment containing that structure was found to affect translation termination in a codon-specific manner. The cause of these effects appeared to be titration of ribosomal protein L11, since normal phenotypes could be restored by simultaneous overproduction of wild-type L11 but not mutant L11. Subsequently, altered termination phenotypes were produced when the availability of L11 was limited by overexpression of RNA antisense to L11 mRNA and, finally, by inactivation of the chromosomal L11 gene, and they too were reversible by simultaneous expression of cloned L11. Our results indicate that in the intact cell the L11BR is an integral functional unit important for translation termination and that the presence of L11 in ribosomes is required for UAG-dependent termination and is somewhat inhibitory of UGA-dependent termination.

journal_name

J Mol Biol

authors

Van Dyke N,Xu W,Murgola EJ

doi

10.1016/S0022-2836(02)00304-2

keywords:

subject

Has Abstract

pub_date

2002-05-31 00:00:00

pages

329-39

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(02)00304-2

journal_volume

319

pub_type

杂志文章
  • Cloning, DNA sequence, functional analysis and transcriptional regulation of the genes encoding dipicolinic acid synthetase required for sporulation in Bacillus subtilis.

    abstract::Dipicolinic acid (DPA) is a small polar molecule that accumulates to high concentrations in bacterial endospores, and is thought to play a role in spore heat resistance, or the maintenance of heat resistance. Previous work has shown that mutations in the spoVF locus of Bacillus subtilis prevent the formation of DPA, a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1403

    authors: Daniel RA,Errington J

    更新日期:1993-07-20 00:00:00

  • Structure, dynamics and thermodynamics of the human centrin 2/hSfi1 complex.

    abstract::Centrin, an EF-hand calcium-binding protein, has been shown to be involved in the duplication of centrosomes, and Sfi1 (Suppressor of fermentation-induced loss of stress resistance protein 1) is one of its centrosomal targets. There are three isoforms of human centrin, but here we only considered centrin 2 (HsCen2). T...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.10.041

    authors: Martinez-Sanz J,Kateb F,Assairi L,Blouquit Y,Bodenhausen G,Abergel D,Mouawad L,Craescu CT

    更新日期:2010-01-08 00:00:00

  • An algorithm for the prediction of proteasomal cleavages.

    abstract::Proteasomes, major proteolytic sites in eukaryotic cells, play an important part in major histocompatibility class I (MHC I) ligand generation and thus in the regulation of specific immune responses. Their cleavage specificity is of outstanding interest for this process. In order to generalize previously determined cl...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3683

    authors: Kuttler C,Nussbaum AK,Dick TP,Rammensee HG,Schild H,Hadeler KP

    更新日期:2000-05-05 00:00:00

  • Rigidification of a flexible protease inhibitor variant upon binding to trypsin.

    abstract::The Tyr35-->Gly replacement in bovine pancreatic trypsin inhibitor (BPTI) has previously been shown to dramatically enhance the flexibility of the trypsin-binding region of the free inhibitor and to destabilize the interaction with the protease by about 3 kcal/mol. The effects of this replacement on the enzyme-inhibit...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.11.003

    authors: Hanson WM,Domek GJ,Horvath MP,Goldenberg DP

    更新日期:2007-02-09 00:00:00

  • Intramolecular recombination of linear DNA catalyzed by the Escherichia coli RecE recombination system.

    abstract::Transformation of different Escherichia coli strains by linear dimers of pBR322 containing different tet alleles was investigated. Linear dimers transformed wild-type strains 0.1 to 1% as efficiently as circular dimers. In contrast, linear dimers transformed recBrecCsbcA strains, where the RecE recombination system is...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90126-3

    authors: Symington LS,Morrison P,Kolodner R

    更新日期:1985-12-05 00:00:00

  • Dystrophin Dp71f associates with the beta1-integrin adhesion complex to modulate PC12 cell adhesion.

    abstract::Dystrophin Dp71 is the main product of the Duchenne muscular dystrophy gene in the brain; however, its function is unknown. To study the role of Dp71 in neuronal cells, we previously generated by antisense treatment PC12 neuronal cell clones with decreased Dp71 expression (antisense-Dp71 cells). PC12 cells express two...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.07.075

    authors: Cerna J,Cerecedo D,Ortega A,García-Sierra F,Centeno F,Garrido E,Mornet D,Cisneros B

    更新日期:2006-10-06 00:00:00

  • The structure of deoxy- and oxy-leghaemoglobin from lupin.

    abstract::The leghaemoglobins have oxygen affinities 11 to 24 times higher than that of sperm whale myoglobin, due mainly to higher rates of association. To find out why, we have determined the structures of deoxy- and oxy-leghaemoglobin II of the lupin at 1.7 A resolution. Results confirm the general features found in previous...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0419

    authors: Harutyunyan EH,Safonova TN,Kuranova IP,Popov AN,Teplyakov AV,Obmolova GV,Rusakov AA,Vainshtein BK,Dodson GG,Wilson JC

    更新日期:1995-08-04 00:00:00

  • (GT)n repetitive tracts affect several stages of RecA-promoted recombination.

    abstract::The effect of GT/CA dinucleotide repeat tracts on RecA-dependent homologous recombination was examined in vitro. By measuring the binding of RecA protein to oligonucleotides containing GT or CA repeats using the surface plasmon resonance (BIAcore), we show that the efficiency of RecA protein binding is sequence depend...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1293

    authors: Dutreix M

    更新日期:1997-10-17 00:00:00

  • A conformational transition at the N terminus of the prion protein features in formation of the scrapie isoform.

    abstract::The scrapie prion protein (PrPSc) is formed from the cellular isoform (PrPC) by a post-translational process that involves a profound conformational change. Linear epitopes for recombinant antibody Fab fragments (Fabs) on PrPC and on the protease-resistant core of PrPSc, designated PrP 27-30, were identified using ELI...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1328

    authors: Peretz D,Williamson RA,Matsunaga Y,Serban H,Pinilla C,Bastidas RB,Rozenshteyn R,James TL,Houghten RA,Cohen FE,Prusiner SB,Burton DR

    更新日期:1997-10-31 00:00:00

  • ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information.

    abstract::Experimental approaches for the identification of functionally important regions on the surface of a protein involve mutagenesis, in which exposed residues are replaced one after another while the change in binding to other proteins or changes in activity are recorded. However, practical considerations limit the use o...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4474

    authors: Armon A,Graur D,Ben-Tal N

    更新日期:2001-03-16 00:00:00

  • Purification and crystallization of the light harvesting LH1 complex from Rhodobacter sphaeroides.

    abstract::The LH1 light harvesting complex has been purified from a mutant of the photosynthetic bacterium Rhodobacter sphaeroides which synthesizes LH1 as the sole pigment protein. Crystallization trials using polyethylene glycol as the precipitant in the presence of the detergent n-octyl glucoside have resulted in the formati...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,收录出版

    doi:10.1016/0022-2836(92)90331-d

    authors: Nunn RS,Artymiuk PJ,Baker PJ,Rice DW,Hunter CN

    更新日期:1992-12-20 00:00:00

  • Crystallization of recA protein from Proteus mirabilis.

    abstract::The recA protein from Proteus mirabilis, which is homologous to the Escherichia coli protein, forms crystals in the orthorhombic space group P2(1)2(1)2(1). There are two 38,000 molecular weight subunits in the asymmetric unit and the unit cell dimensions are a = 57.5, b = 127.0 and c = 157.0 A. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(86)90486-9

    authors: Weber IT,Steitz TA

    更新日期:1986-03-05 00:00:00

  • Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding.

    abstract::Biogenesis of β-barrel membrane proteins is a complex, multistep, and as yet incompletely characterized process. The bacterial porin family is perhaps the best-studied protein family among β-barrel membrane proteins that allows diffusion of small solutes across the bacterial outer membrane. In this study, we have iden...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2012.02.043

    authors: Naveed H,Jimenez-Morales D,Tian J,Pasupuleti V,Kenney LJ,Liang J

    更新日期:2012-05-25 00:00:00

  • Co-optimization of ribozyme substrate stacking and L-arginine binding.

    abstract::A model of the Tetrahymena catalytic site predicts that nucleotide 262 (nt262) caps an RNA pocket in which nucleoside substrates and arginine-like competitive inhibitors reside. Here we show that substituted RNAs behave as if nt262 stacks on nucleoside substrates, supporting the model. The more frequent an nt262 is in...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90095-2

    authors: Yarus M,Majerfeld I

    更新日期:1992-06-20 00:00:00

  • The Role of zinc in the disulphide stress-regulated anti-sigma factor RsrA from Streptomyces coelicolor.

    abstract::The regulation of disulphide stress in actinomycetes such as Streptomyces coelicolor is known to involve the zinc-containing anti-sigma factor RsrA that binds and inactivates the redox-regulated sigma factor sigmaR. However, it is not known how RsrA senses disulphide stress nor what role the metal ion plays. Using in ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.08.038

    authors: Li W,Bottrill AR,Bibb MJ,Buttner MJ,Paget MS,Kleanthous C

    更新日期:2003-10-17 00:00:00

  • Calculation of the relative binding free energy of 2'GMP and 2'AMP to ribonuclease T1 using molecular dynamics/free energy perturbation approaches.

    abstract::We present a calculation of the relative changes in binding free energy between the complex of ribonuclease T1 (RNase Tr) with its inhibitor 2'-guanosine monophosphate (2'GMP) and that of RNase T1-2'-adenosine monophosphate (2'AMP) by means of a thermodynamic perturbation method implemented with molecular dynamics. Us...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(90)90315-D

    authors: Hirono S,Kollman PA

    更新日期:1990-03-05 00:00:00

  • Kinetic control in protein folding for light chain amyloidosis and the differential effects of somatic mutations.

    abstract::Light chain amyloidosis is a devastating disease where immunoglobulin light chains form amyloid fibrils, resulting in organ dysfunction and death. Previous studies have shown a direct correlation between the protein thermodynamic stability and the propensity for amyloid formation for some proteins involved in light ch...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.10.016

    authors: Blancas-Mejía LM,Tischer A,Thompson JR,Tai J,Wang L,Auton M,Ramirez-Alvarado M

    更新日期:2014-01-23 00:00:00

  • HIV-1 nucleocapsid protein as a nucleic acid chaperone: spectroscopic study of its helix-destabilizing properties, structural binding specificity, and annealing activity.

    abstract::Assembly of infectious retroviral particles involves recognition of specific sequences on the viral RNA by the nucleocapsid (NC) domain of the Gag polyprotein, and subsequent stoichiometric binding of the processed NC protein along the entire length of the RNA. NC proteins also act as nucleic acid chaperones. They acc...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/S0022-2836(02)00043-8

    authors: Urbaneja MA,Wu M,Casas-Finet JR,Karpel RL

    更新日期:2002-05-03 00:00:00

  • Mutations in beta-myosin S2 that cause familial hypertrophic cardiomyopathy (FHC) abolish the interaction with the regulatory domain of myosin-binding protein-C.

    abstract::The myosin filaments of striated muscle contain a family of enigmatic myosin-binding proteins (MyBP), MyBP-C and MyBP-H. These modular proteins of the intracellular immunoglobulin superfamily contain unique domains near their N termini. The N-terminal domain of cardiac MyBP-C, the MyBP-C motif, contains additional pho...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2522

    authors: Gruen M,Gautel M

    更新日期:1999-02-26 00:00:00

  • Contextual constraints on synonymous codon choice.

    abstract::We have studied the statistical constraints on synonymous codon choice to evaluate various proposals regarding the origin of the bias in synonymous codon usage observed by Fiers et al. (1975), Air et al. (1976), Grantham et al. (1980) and others. We have determined the statistical dependence of the degenerate third ba...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(83)90063-3

    authors: Lipman DJ,Wilbur WJ

    更新日期:1983-01-25 00:00:00

  • Crystal structure of three consecutive laminin-type epidermal growth factor-like (LE) modules of laminin gamma1 chain harboring the nidogen binding site.

    abstract::The structure of three consecutive laminin-type EGF-like (LE) modules of mouse laminin gammma1 chain, gamma1III3-5 (positions 738 to 899), has been determined by multiple isomorphous replacement in a crystal of space group p6(4)22 (a=b=74.57 angstroms, c = 185.11 angstroms and gamma = 120 degrees). The crystal structu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0191

    authors: Stetefeld J,Mayer U,Timpl R,Huber R

    更新日期:1996-04-05 00:00:00

  • Preliminary X-ray crystallographic studies of ribonuclease I from Escherichia coli.

    abstract::Single crystals of ribonuclease I from Escherichia coli have been obtained by the vapor diffusion method. The crystals belong to the tetragonal space group P4(1)2(1)2 or its enantiomer P4(3)2(1)2 and have cell parameters a = b = 119.01 A and c = 34.40 A. There is one 27,000 dalton monomer in the asymmetric unit. The c...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1603

    authors: Lim LW,Mathur S,Cannistraro VJ,Kennell D

    更新日期:1993-11-20 00:00:00

  • In crystallo capture of a Michaelis complex and product-binding modes of a bacterial phosphotriesterase.

    abstract::The mechanism by which the binuclear metallophosphotriesterases (PTEs, E.C. 3.1.8.1) catalyse substrate hydrolysis has been extensively studied. The mu-hydroxo bridge between the metal ions has been proposed to be the initiating nucleophile in the hydrolytic reaction. In contrast, analysis of some biomimetic systems h...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.10.061

    authors: Jackson CJ,Foo JL,Kim HK,Carr PD,Liu JW,Salem G,Ollis DL

    更新日期:2008-02-01 00:00:00

  • A structural perspective of the sequence variability within botulinum neurotoxin subtypes A1-A4.

    abstract::Botulinum neurotoxin (BoNT) is a category A toxin that has been classified within seven serotypes, designated A-G. Recently, it has been discovered that sequence variability occurs in BoNTs produced by serotype A (BoNT/A) variant strains, designated as subtypes A1 and A2, which have significantly different antibody-bi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.07.040

    authors: Arndt JW,Jacobson MJ,Abola EE,Forsyth CM,Tepp WH,Marks JD,Johnson EA,Stevens RC

    更新日期:2006-09-29 00:00:00

  • Mismatch repair factor MSH2-MSH3 binds and alters the conformation of branched DNA structures predicted to form during genetic recombination.

    abstract::Genetic studies in Saccharomyces cerevisiae predict that the mismatch repair (MMR) factor MSH2-MSH3 binds and stabilizes branched recombination intermediates that form during single strand annealing and gene conversion. To test this model, we constructed a series of DNA substrates that are predicted to form during the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.05.032

    authors: Surtees JA,Alani E

    更新日期:2006-07-14 00:00:00

  • Projection structures of three photosynthetic complexes from Rhodobacter sphaeroides: LH2 at 6 A, LH1 and RC-LH1 at 25 A.

    abstract::Three photosynthetic complexes, light-harvesting complex 2 (LH2), light-harvesting complex 1 (LH1), and the reaction centre-light-harvesting complex 1 photounit (RC-LH1), were purified from a single species of a purple bacterium, Rhodobacter sphaeroides, and reconstituted into two-dimensional (2-D) crystals. Vesicular...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2050

    authors: Walz T,Jamieson SJ,Bowers CM,Bullough PA,Hunter CN

    更新日期:1998-10-02 00:00:00

  • Electrostatic contributions to the stability of halophilic proteins.

    abstract::Examination of the first crystal structures of proteins from a halophilic organism suggests that an abundance of acidic residues distributed over the protein surface is a key determinant of adaptation to high-salt conditions. Although one extant theory suggests that acidic residues are favored because of their superio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1904

    authors: Elcock AH,McCammon JA

    更新日期:1998-07-24 00:00:00

  • Stochastic switching in gene networks can occur by a single-molecule event or many molecular steps.

    abstract::Due to regulatory feedback, biological networks can exist stably in multiple states, leading to heterogeneous phenotypes among genetically identical cells. Random fluctuations in protein numbers, tuned by specific molecular mechanisms, have been hypothesized to drive transitions between these different states. We deve...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.11.035

    authors: Choi PJ,Xie XS,Shakhnovich EI

    更新日期:2010-02-12 00:00:00

  • Structural polymorphism of Methanothermobacter thermautotrophicus MCM.

    abstract::The minichromosome maintenance (MCM) proteins are essential for replication initiation and elongation in eukarya and archaea. There are six MCM proteins in eukaryotes, and MCM complexes are believed to unwind DNA during chromosomal DNA replication. However, the mechanism and structure of the MCM complexes are not know...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.11.076

    authors: Chen YJ,Yu X,Kasiviswanathan R,Shin JH,Kelman Z,Egelman EH

    更新日期:2005-02-18 00:00:00

  • A structural-informatics approach for mining beta-sheets: locating sheets in intermediate-resolution density maps.

    abstract::Here, we report a new computational method, called sheetminer, for mining beta-sheets in the density maps at intermediate resolutions of 6 to 10A. The method employs a multi-step ad hoc morphological analysis of density maps to identify the unique characteristics of beta-sheets. It was tested on density maps from 12 p...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00859-3

    authors: Kong Y,Ma J

    更新日期:2003-09-12 00:00:00