Structural dynamics of translating ribosomes: 16S ribosomal RNA bases that may move twice during translocation.

Abstract:

:Recent footprinting, sedimentation and neutron-scattering results obtained in vivo or on pre-translocation and post-translocation ribosomal complexes are integrated with cross-linking and immunoelectron microscopy information. It is proposed that the 30S subunit pulses during translocation and that its pre- and post-translocation structures are not necessarily identical. Accordingly, translocation is characterized by three consecutive conformational states of the 30S and 50S subunits. State 1 (the pre-translocation state) lasts until the elongation factor EF-G.GTP complex binds to the ribosome or adopts the GTPase conformation. State 2 (the translocation state, or the peak or plateau of the pulse) follows and lasts until EF-G adopts a subsequent conformation or is released from the ribosome. State 3 (the post-translocation state) ensues and lasts until A (aminoacyl) site binding of aminoacyl-tRNA. In state 2, 16S RNA hairpins 26 and 33-33A, located in the platform and the head of the 30S subunit, respectively, become kinked or twisted, and residue A1503, near the decoding site, becomes exposed. A platform twist is associated with P (peptide) to E (exit) site tRNA movements and a head twist with pivoting of the peptidyl-tRNA elbow from the A to the P site, around a (retractable?) S19 domain. These twists result in an unlocking of the platform and the head from the 50S subunit. Exposure of A1503 is tentatively associated with movements of mRNA or tRNA anticodon stem-loops. These twisted or otherwise-exposed residues readopt their previous setting upon completion of translocation, i.e. states 1 and 3 of 16S RNA differ more from state 2 than from each other.(ABSTRACT TRUNCATED AT 250 WORDS)

journal_name

Mol Microbiol

journal_title

Molecular microbiology

authors

Laughrea M

doi

10.1111/j.1365-2958.1994.tb00378.x

subject

Has Abstract

pub_date

1994-03-01 00:00:00

pages

999-1007

issue

6

eissn

0950-382X

issn

1365-2958

journal_volume

11

pub_type

杂志文章,评审
  • DNA topology of highly transcribed operons in Salmonella enterica serovar Typhimurium.

    abstract::Bacteria differ from eukaryotes by having the enzyme DNA gyrase, which catalyses the ATP-dependent negative supercoiling of DNA. Negative supercoils are essential for condensing chromosomes into an interwound (plectonemic) and branched structure known as the nucleoid. Topo-1 removes excess supercoiling in an ATP-indep...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2010.07394.x

    authors: Booker BM,Deng S,Higgins NP

    更新日期:2010-12-01 00:00:00

  • Different residues in periplasmic domains of the CcmC inner membrane protein of Pseudomonas fluorescens ATCC 17400 are critical for cytochrome c biogenesis and pyoverdine-mediated iron uptake.

    abstract::The inner membrane protein CcmC (CytA) of Pseudomonas fluorescens ATCC17400, which has homologues in several bacteria and plant mitochondria, is needed for the biogenesis of cytochrome c. A CcmC-deficient mutant is also compromised in the production and utilization of pyoverdine, the high-affinity fluorescent sideroph...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.1998.01085.x

    authors: Gaballa A,Baysse C,Koedam N,Muyldermans S,Cornelis P

    更新日期:1998-11-01 00:00:00

  • Hfq reduces envelope stress by controlling expression of envelope-localized proteins and protein complexes in enteropathogenic Escherichia coli.

    abstract::Gram-negative bacteria possess several envelope stress responses that detect and respond to damage to this critical cellular compartment. The σ(E) envelope stress response senses the misfolding of outer membrane proteins (OMPs), while the Cpx two-component system is believed to detect the misfolding of periplasmic and...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.12581

    authors: Vogt SL,Raivio TL

    更新日期:2014-05-01 00:00:00

  • Regulation of glutamate dehydrogenase expression in Pseudomonas putida results from its direct repression by NtrC under nitrogen-limiting conditions.

    abstract::Nitrogen-regulated genes in enterobacteria are positively controlled by the transcriptional activator of σ(N) -dependent promoters NtrC, either directly or indirectly, through the dual regulator Nac. Similar to enterobacteria, gdhA encoding glutamate dehydrogenase from Pseudomonas putida is one of the few genes that i...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2010.07329.x

    authors: Hervás AB,Canosa I,Santero E

    更新日期:2010-10-01 00:00:00

  • Determination of a specific region of the purine-cytosine permease involved in the recognition of its substrates.

    abstract::Three u.v.-induced mutants of the purine-cytosine permease gene of Saccharomyces cerevisiae, with altered apparent Michaelis constant of transport (Kmapp), were cloned and sequenced. One of the mutants had extensive nucleotide replacement, whereas the other two had a single mutation. To evaluate the contribution of th...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.1992.tb01757.x

    authors: Bloch JC,Sychrova H,Souciet JL,Jund R,Chevallier MR

    更新日期:1992-10-01 00:00:00

  • New erythromycin derivatives from Saccharopolyspora erythraea using sugar O-methyltransferases from the spinosyn biosynthetic gene cluster.

    abstract::Using a previously developed expression system based on the erythromycin-producing strain of Saccharopolyspora erythraea, O-methyltransferases from the spinosyn biosynthetic gene cluster of Saccharopolyspora spinosa have been shown to modify a rhamnosyl sugar attached to a 14-membered polyketide macrolactone. The spnI...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2001.02594.x

    authors: Gaisser S,Lill R,Wirtz G,Grolle F,Staunton J,Leadlay PF

    更新日期:2001-09-01 00:00:00

  • Low-molecular-weight post-translationally modified microcins.

    abstract::Microcins are a class of ribosomally synthesized antibacterial peptides produced by Enterobacteriaceae and active against closely related bacterial species. While some microcins are active as unmodified peptides, others are heavily modified by dedicated maturation enzymes. Low-molecular-weight microcins from the post-...

    journal_title:Molecular microbiology

    pub_type: 杂志文章,评审

    doi:10.1111/j.1365-2958.2007.05874.x

    authors: Severinov K,Semenova E,Kazakov A,Kazakov T,Gelfand MS

    更新日期:2007-09-01 00:00:00

  • The rpf gene of Micrococcus luteus encodes an essential secreted growth factor.

    abstract::Micrococcus luteus secretes a small protein called Rpf, which has autocrine and paracrine signalling functions and is required for the resuscitation of dormant cells. Originally isolated from the supernatant of actively growing cultures, Rpf was also detected on the surface of actively growing bacteria. Most molecules...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2002.03183.x

    authors: Mukamolova GV,Turapov OA,Kazarian K,Telkov M,Kaprelyants AS,Kell DB,Young M

    更新日期:2002-11-01 00:00:00

  • Malaria transmission-blocking antigen, Pfs230, mediates human red blood cell binding to exflagellating male parasites and oocyst production.

    abstract::Malaria transmission requires that the parasites differentiate into gametocytes prior to ingestion by a mosquito during a blood meal. Once in the mosquito midgut the gametocytes emerge from red blood cells (RBCs), fertilize, develop into ookinetes and finally infectious sporozoites. Gamete surface antigen, Pfs230, is ...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2006.05284.x

    authors: Eksi S,Czesny B,van Gemert GJ,Sauerwein RW,Eling W,Williamson KC

    更新日期:2006-08-01 00:00:00

  • RepC protein of the octopine-type Ti plasmid binds to the probable origin of replication within repC and functions only in cis.

    abstract::Vegetative replication and partitioning of many plasmids and some chromosomes of alphaproteobacteria are directed by their repABC operons. RepA and RepB proteins direct the partitioning of replicons to daughter cells, while RepC proteins are replication initiators, although they do not resemble any characterized repli...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2011.07789.x

    authors: Pinto UM,Flores-Mireles AL,Costa ED,Winans SC

    更新日期:2011-09-01 00:00:00

  • Mycobacterium tuberculosis EspB binds phospholipids and mediates EsxA-independent virulence.

    abstract::The type-VII ESX-1 secretion apparatus, encoded by the esx-1 genetic locus, is essential for the export of EsxA and EsxB, two major virulence factors of Mycobacterium tuberculosis. ESX-1 also requires the products of the unlinked espACD operon for optimal function and these proteins are considered integral parts of th...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.12336

    authors: Chen JM,Zhang M,Rybniker J,Boy-Röttger S,Dhar N,Pojer F,Cole ST

    更新日期:2013-09-01 00:00:00

  • Cytotoxic activity of a recombinant chimaeric protein between Pseudomonas aeruginosa exotoxin A and Corynebacterium diphtheriae diphtheria toxin.

    abstract::A segment of the exotoxin A gene of Pseudomonas aeruginosa, coding for the N-terminal end of domain I and domain II of the toxin (ETA), was genetically fused to the diphtheria toxin gene of Corynebacterium diphtheriae, coding for the N-terminal end of A fragment of diphtheria toxin (DT). The resulting hybrid protein (...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.1992.tb00849.x

    authors: Guidi-Rontani C

    更新日期:1992-05-01 00:00:00

  • The HypB protein from Bradyrhizobium japonicum can store nickel and is required for the nickel-dependent transcriptional regulation of hydrogenase.

    abstract::The HypB protein from Bradyrhizobium japonicum is a metal-binding GTPase required for hydrogenase expression. In-frame mutagenesis of hypB resulted in strains that were partially or completely deficient in hydrogenase expression, depending on the degree of disruption of the gene. Complete deletion of the gene yielded ...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.1997.3251690.x

    authors: Olson JW,Fu C,Maier RJ

    更新日期:1997-04-01 00:00:00

  • EspA, a protein secreted by enteropathogenic Escherichia coli, is required to induce signals in epithelial cells.

    abstract::Enteropathogenic Escherichia coli (EPEC) is a leading cause of infant diarrhoea. EPEC mediates several effects on host epithelial cells, including activation of signal-transduction pathways, cytoskeletal rearrangement along with pedestal and attaching/effacing lesion formation. It has been previously shown that the EP...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.1996.tb02619.x

    authors: Kenny B,Lai LC,Finlay BB,Donnenberg MS

    更新日期:1996-04-01 00:00:00

  • Pentapeptide-rich peptidoglycan at the Bacillus subtilis cell-division site.

    abstract::Peptidoglycan (PG), the major component of the bacterial cell wall, is one large macromolecule. To allow for the different curvatures of PG at cell poles and division sites, there must be local differences in PG architecture and eventually also chemistry. Here we report such local differences in the Gram-positive rod-...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.13629

    authors: Morales Angeles D,Liu Y,Hartman AM,Borisova M,de Sousa Borges A,de Kok N,Beilharz K,Veening JW,Mayer C,Hirsch AK,Scheffers DJ

    更新日期:2017-04-01 00:00:00

  • The essential role of the invariant GGQ motif in the function and stability in vivo of bacterial release factors RF1 and RF2.

    abstract::Release factors RF1 and RF2 are required in bacteria for the cleavage of peptidyl-tRNA. A single sequence motif, GGQ, is conserved in all eubacterial, archaebacterial and eukaryotic release factors and may mimic the CCA end of tRNA, although the position of the motif in the crystal structures of human eRF1 and Escheri...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2003.03301.x

    authors: Mora L,Heurgué-Hamard V,Champ S,Ehrenberg M,Kisselev LL,Buckingham RH

    更新日期:2003-01-01 00:00:00

  • Two operons that encode FNR-like proteins in Lactococcus lactis.

    abstract::Global regulatory circuits of the type mediated by CRP and FNR in Escherichia coli were sought in Lactococcus lactis to provide a basis for redirecting carbon metabolism to specific fermentation products. Using a polymerase chain reaction (PCR) approach, two genes (flpA and flpB) encoding FNR-like proteins (FlpA and F...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.1999.01298.x

    authors: Gostick DO,Griffin HG,Shearman CA,Scott C,Green J,Gasson MJ,Guest JR

    更新日期:1999-03-01 00:00:00

  • Novel coordination of lipopolysaccharide modifications in Vibrio cholerae promotes CAMP resistance.

    abstract::In the environment and during infection, the human intestinal pathogen Vibrio cholerae must overcome noxious compounds that damage the bacterial outer membrane. The El Tor and classical biotypes of O1 V. cholerae show striking differences in their resistance to membrane disrupting cationic antimicrobial peptides (CAMP...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.13835

    authors: Herrera CM,Henderson JC,Crofts AA,Trent MS

    更新日期:2017-11-01 00:00:00

  • Conversion of an extracellular cytolysin into a phagosome-specific lysin which supports the growth of an intracellular pathogen.

    abstract::Listeria monocytogenes is a facultative intracellular pathogen which secretes a pore-forming cytolysin, listeriolysin O (LLO), necessary for intracellular growth. Clostridium perfringens is an extracellular pathogen which secretes a related cytolysin, perfringolysin O (PFO). When PFO is secreted by intracellular L. mo...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.1996.00074.x

    authors: Jones S,Preiter K,Portnoy DA

    更新日期:1996-09-01 00:00:00

  • A sirtuin in the African trypanosome is involved in both DNA repair and telomeric gene silencing but is not required for antigenic variation.

    abstract::Silent information regulator 2 (Sir2)-related proteins or sirtuins function as NAD(+)-dependent deacetylases or ADP ribosylases that target a range of substrates, thereby influencing chromatin structure and a diverse range of other biological functions. Genes encoding three Sir2-related proteins (SIR2rp1-3) have been ...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2006.05553.x

    authors: Alsford S,Kawahara T,Isamah C,Horn D

    更新日期:2007-02-01 00:00:00

  • Chlorinated phenols control the expression of the multidrug resistance efflux pump MexAB-OprM in Pseudomonas aeruginosa by interacting with NalC.

    abstract::NalC is a TetR type regulator that represses the multidrug efflux pump MexAB-OprM in Pseudomonas aeruginosa. Here we explain the mechanism of NalC-mediated regulation of MexAB-OprM. We show that NalC non-covalently binds chlorinated phenols and chemicals containing chlorophenol side-chains such as triclosan. NalC-chlo...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2011.07544.x

    authors: Ghosh S,Cremers CM,Jakob U,Love NG

    更新日期:2011-03-01 00:00:00

  • Clostridium difficile toxin expression is inhibited by the novel regulator TcdC.

    abstract::Clostridium difficile, an emerging nosocomial pathogen of increasing clinical significance, produces two large protein toxins that are responsible for the cellular damage associated with the disease. The precise mechanisms by which toxin synthesis is regulated in response to environmental change have yet to be discove...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2007.05739.x

    authors: Matamouros S,England P,Dupuy B

    更新日期:2007-06-01 00:00:00

  • Bacterial genetics by flow cytometry: rapid isolation of Salmonella typhimurium acid-inducible promoters by differential fluorescence induction.

    abstract::The ability of Salmonella typhimurium to survive and replicate within murine macrophages is dependent on a low phagosomal pH. This requirement for an acidic vacuole suggests that low pH is an important environmental stimulus for the transcription of genes necessary for intracellular survival. To study the behaviour of...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.1996.00120.x

    authors: Valdivia RH,Falkow S

    更新日期:1996-10-01 00:00:00

  • The role of a stress-response protein in Salmonella typhimurium virulence.

    abstract::We recently described the use of selective transposon mutagenesis to generate a series of avirulent mutants of a pathogenic strain of Salmonella typhimurium. Cloning and sequencing of the insertion sites from two of these mutants reveals that both have identical locations within an open reading frame that is highly ho...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.1991.tb02122.x

    authors: Johnson K,Charles I,Dougan G,Pickard D,O'Gaora P,Costa G,Ali T,Miller I,Hormaeche C

    更新日期:1991-02-01 00:00:00

  • Organization of the genes necessary for hydrogenase expression in Rhodobacter capsulatus. Sequence analysis and identification of two hyp regulatory mutants.

    abstract::A 25 kbp DNA fragment from the chromosome of Rhodobacter capsulatus B10 carrying hydrogenase (hup) determinants was completely sequenced. Coding regions corresponding to 20 open reading frames were identified. The R. capsulatus hydrogenase-specific gene (hup and hyp) products bear significant structural identity to hy...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.1993.tb01199.x

    authors: Colbeau A,Richaud P,Toussaint B,Caballero FJ,Elster C,Delphin C,Smith RL,Chabert J,Vignais PM

    更新日期:1993-04-01 00:00:00

  • Interaction of the sensor module of Mycobacterium tuberculosis H37Rv KdpD with members of the Lpr family.

    abstract::The genetic and biochemical mechanisms by which Mycobacterium tuberculosis senses and responds to the complex environment that it encounters during infection and persistence within the host remain unknown. In a number of bacterial species, the Kdp signal transduction pathway appears to be the primary response to envir...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2003.03356.x

    authors: Steyn AJ,Joseph J,Bloom BR

    更新日期:2003-02-01 00:00:00

  • Identification of a multifunctional protein, PhaM, that determines number, surface to volume ratio, subcellular localization and distribution to daughter cells of poly(3-hydroxybutyrate), PHB, granules in Ralstonia eutropha H16.

    abstract::A two-hybrid approach was applied to screen for proteins with the ability to interact with PHB synthase (PhaC1) of Ralstonia eutropha. The H16_A0141 gene (phaM) was identified in the majority of positive clones. PhaM (26.6 kDa) strongly interacted with PhaC1 and with phasin PhaP5 but not with PhaP1 or other PHB granul...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2011.07869.x

    authors: Pfeiffer D,Wahl A,Jendrossek D

    更新日期:2011-11-01 00:00:00

  • One if by land, two if by sea: signalling to the ranks with CSP and XIP.

    abstract::In many streptococci, quorum sensing utilizes secreted, linear peptides that engage cognate receptors to coordinate gene expression among members of a local population. Streptococcus mutans employs the secreted peptides CSP and XIP to stimulate production of antimicrobial bacteriocins and to induce development of comp...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.12029

    authors: Federle MJ,Morrison DA

    更新日期:2012-10-01 00:00:00

  • Differential decay of a polycistronic Escherichia coli transcript is initiated by RNaseE-dependent endonucleolytic processing.

    abstract::Differential expression of the genes expressing Pap pili in Escherichia coli was suggested to involve mRNAs with different stabilities. As the result of a post-transcriptional processing event, a papA gene-specific mRNA product (mRNA-A) accumulates in large excess relative to the primary mRNA-BA transcript. Our result...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.1991.tb01928.x

    authors: Nilsson P,Uhlin BE

    更新日期:1991-07-01 00:00:00

  • 'Form variation' of the O12 antigen is critical for persistence of Salmonella Typhimurium in the murine intestine.

    abstract::Salmonella enterica subspecies I serotypes are responsible for the vast majority of salmonellosis in mammals and birds, yet only a few factors specific to this group that allow them to persist in this niche have been identified. We show that STM0557, a S. enterica subspecies I-specific gene encoding an inner membrane ...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2008.06461.x

    authors: Bogomolnaya LM,Santiviago CA,Yang HJ,Baumler AJ,Andrews-Polymenis HL

    更新日期:2008-12-01 00:00:00