RNase E and polyadenyl polymerase I are involved in maturation of CI RNA, the P4 phage immunity factor.


:Bacteriophage P4 immunity is controlled by a small stable RNA (CI RNA) that derives from the processing of primary transcripts. In previous works, we observed that the endonuclease RNase P is required for the maturation of CI RNA 5'-end; moreover, we found that polynucleotide phosphorylase (PNPase), a 3' to 5' RNA-degrading enzyme, is required for efficient 5'-end processing of CI RNA, suggesting that 3'-end degradation of the primary transcript might be involved in the production of proper RNase P substrates. Here, we demonstrate that another Escherichia coli nuclease, RNase E, would appear to be involved in this process. We found that transcripts of the P4 immunity region are modified by the post-transcriptional addition of short poly(A) tails and heteropolymeric tails with prevalence of A residues. Most oligoadenylated transcripts encompass the whole cI locus and are thus compatible as intermediates in the CI RNA maturation pathway. On the contrary, in a polynucleotide phosphorylase (PNPase)-defective host, adenylation occurred most frequently within cI, implying that such transcripts are targeted for degradation. We did not find polyadenylation in a pcnB mutant, suggesting that the pcnB-encoded polyadenyl polymerase I (PAP I) is the only enzyme responsible for modification of P4 immunity transcripts. Maturation of CI RNA 5'-end in such a mutant was impaired, further supporting the idea that processing of the 3'-end of primary transcripts is an important step for efficient maturation of CI RNA by RNase P.


J Mol Biol


Briani F,Del Vecchio E,Migliorini D,Hajnsdorf E,Régnier P,Ghisotti D,Dehò G





Has Abstract


2002-04-26 00:00:00














  • Genome-wide survey of prokaryotic O-protein phosphatases.

    abstract::Complex and diverse signal transduction circuits are responsible for the efficient functioning of cellular network. Protein kinases and O-protein phosphatases are primarily responsible for propagating such stimuli within a eukaryotic cell. However, there is limited understanding of O-protein phosphatases in the prokar...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Bhaduri A,Sowdhamini R

    更新日期:2005-09-23 00:00:00

  • An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints.

    abstract::A novel approach aiding in the prediction of RNA secondary structures is presented. Although phylogenetic methods are the most successful at deriving RNA secondary structures, the are not applicable when the number of sequences or the sequence variability is too low. Methods based on energy minimization are therefore ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Gaspin C,Westhof E

    更新日期:1995-11-24 00:00:00

  • Molecular evolution of multisubunit RNA polymerases: sequence analysis.

    abstract::Transcription in all cellular organisms is performed by multisubunit, DNA-dependent RNA polymerases that synthesize RNA from DNA templates. Previous sequence and structural studies have elucidated the importance of shared regions common to all multisubunit RNA polymerases. In addition, RNA polymerases contain multiple...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Lane WJ,Darst SA

    更新日期:2010-01-29 00:00:00

  • Computational and experimental probes of symmetry mismatches in the Arc repressor-DNA complex.

    abstract::Arc repressor from bacteriophage P22 is a homodimeric member of the ribbon-helix-helix family of transcription factors. Two dimers bind cooperatively to adjacent sites on operator DNA with the antiparallel beta-sheet of each Arc dimer contacting the major groove. Despite the 2-fold symmetry of the dimer, the sequence ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Spector S,Sauer RT,Tidor B

    更新日期:2004-07-02 00:00:00

  • The Helicobacter pylori CagD (HP0545, Cag24) protein is essential for CagA translocation and maximal induction of interleukin-8 secretion.

    abstract::Pathogenic strains of Helicobacter pylori use a type IV secretion system (T4SS) to deliver the toxin CagA into human host cells. The T4SS, along with the toxin itself, is coded into a genomic insert, which is termed the cag pathogenicity island. The cag pathogenicity island contains about 30 open-reading frames, for m...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Cendron L,Couturier M,Angelini A,Barison N,Stein M,Zanotti G

    更新日期:2009-02-13 00:00:00

  • Role of Microglia in Ataxias.

    abstract::Microglia, the resident macrophages of the central nervous system, critically influence neural function during development and in adulthood. Microglia are also profoundly sensitive to insults to the brain to which they respond with process of activation that includes spectrum of changes in morphology, function, and ge...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审


    authors: Ferro A,Sheeler C,Rosa JG,Cvetanovic M

    更新日期:2019-04-19 00:00:00

  • Refined crystal structure of beta-lactamase from Staphylococcus aureus PC1 at 2.0 A resolution.

    abstract::The crystal structure of a class A beta-lactamase from Staphylococcus aureus PC1 has been refined at 2.0 A resolution. The resulting crystallographic R-factor (R = sigma h parallel Fo[-]Fc parallel/sigma h[Fo], where [Fo] and [Fc] are the observed and calculated structure factor amplitudes, respectively), is 0.163 for...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Herzberg O

    更新日期:1991-02-20 00:00:00

  • The catalytic subunit of human protein kinase CK2 structurally deviates from its maize homologue in complex with the nucleotide competitive inhibitor emodin.

    abstract::The Ser/Thr kinase CK2 (former name: casein kinase 2) is a heterotetrameric enzyme composed of two catalytic chains (CK2alpha) attached to a dimer of noncatalytic subunits. Together with the cyclin-dependent kinases and the mitogen-activated protein kinases, CK2alpha belongs to the CMGC family of the eukaryotic protei...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Raaf J,Klopffleisch K,Issinger OG,Niefind K

    更新日期:2008-03-14 00:00:00

  • Structure and Function of Viral Deubiquitinating Enzymes.

    abstract::Post-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including innate and adaptive immune responses. Ubiquitin-mediated control over these processes can be reversed by cellular deubiquitinating enzymes (DUBs), which remove ubiquitin from cellular targets and depolyme...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审


    authors: Bailey-Elkin BA,Knaap RCM,Kikkert M,Mark BL

    更新日期:2017-11-10 00:00:00

  • The eta-globin gene. Its long evolutionary history in the beta-globin gene family of mammals.

    abstract::In phylogenetic reconstructions by the parsimony method, utilizing 62 sequenced globin genes and pseudogenes (including 34 of the beta-globin gene family from eutherian orders Primates, Lagomorpha, Artiodactyla and Rodentia), the branch of primate psi beta pseudogenes and the goat embryonically expressed epsilon II ge...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Goodman M,Koop BF,Czelusniak J,Weiss ML

    更新日期:1984-12-25 00:00:00

  • In-vivo degradation pathway of an excised intervening sequence.

    abstract::A study of the distribution in heterogeneous nuclear RNP (hnRNP) of the different forms of the first intervening sequence (IVSI) from the E3 transcription unit of adenovirus serotype 2 suggests a three-step pathway for IVS excision and degradation. First, the lariat IVS is formed in a large RNP of the size of premesse...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Sittler A,Gallinaro H,Kister L,Jacob M

    更新日期:1987-10-20 00:00:00

  • DNA polymerase X from African swine fever virus: quantitative analysis of the enzyme-ssDNA interactions and the functional structure of the complex.

    abstract::Interactions of polymerase X from African swine fever virus with single-stranded DNA (ssDNA) have been studied, using quantitative fluorescence titration and analytical ultracentrifugation techniques. Experiments were performed with a fluorescent etheno-derivative of ssDNA oligomers. Studies of unmodified ssDNA oligom...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Jezewska MJ,Marcinowicz A,Lucius AL,Bujalowski W

    更新日期:2006-02-10 00:00:00

  • Modular structure, local flexibility and cold-activity of a novel chitobiase from a psychrophilic Antarctic bacterium.

    abstract::The gene archb encoding for the cell-bound chitobiase from the Antarctic Gram-positive bacterium Arthrobacter sp. TAD20 was cloned and expressed in Escherichia coli in a soluble form. The mature chitobiase ArChb possesses four functionally independent domains: a catalytic domain stabilized by Ca(2+), a galactose-bindi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Lonhienne T,Zoidakis J,Vorgias CE,Feller G,Gerday C,Bouriotis V

    更新日期:2001-07-06 00:00:00

  • Interdomain contact regions and angles between adjacent short consensus repeat domains.

    abstract::The short consensus repeat domain (SCR, complement control protein module, sushi-domain) is a structural unit found in multiple adjacent copies in more than 40 human proteins. Each bead-like domain is composed of approximately 60 residues and the adjacent domains are connected in a head-to-tail fashion with linkers th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Lehtinen MJ,Meri S,Jokiranta TS

    更新日期:2004-12-10 00:00:00

  • Role of electrostatic repulsion in the acidic molten globule of cytochrome c.

    abstract::The molten globule has been assumed to be a major intermediate state of protein folding. To extend our understanding of protein folding it is important to elucidate the thermodynamic mechanism of conformational stability of the molten globule. To clarify the role of electrostatic charge repulsion in the stability of t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Goto Y,Nishikiori S

    更新日期:1991-12-05 00:00:00

  • Lipid molecules induce p38α activation via a novel molecular switch.

    abstract::p38α mitogen-activated protein kinase (MAPK) is generally activated by dual phosphorylation but has also been shown to exhibit alternative activation modes. One of these modes included a direct interaction with phosphatidylinositol ether lipid analogues (PIA) inducing p38α autoactivation and apoptosis. Perifosine, an ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Tzarum N,Eisenberg-Domovich Y,Gills JJ,Dennis PA,Livnah O

    更新日期:2012-12-14 00:00:00

  • Molecular interplay between RNA polymerase and two transcriptional regulators in promoter switch.

    abstract::Transcription regulation relies in the molecular interplay between the RNA polymerase (RNAP) and regulatory factors. Phage phi29 promoters A2c, A2b and A3 are coordinately regulated by the transcriptional regulator protein p4 and the histone-like protein p6. This study shows that protein p4 binds simultaneously to fou...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Camacho A,Salas M

    更新日期:2004-02-13 00:00:00

  • Lagging strand synthesis in coordinated DNA synthesis by bacteriophage t7 replication proteins.

    abstract::The proteins of bacteriophage T7 DNA replication mediate coordinated leading and lagging strand synthesis on a minicircle template. A distinguishing feature of the coordinated synthesis is the presence of a replication loop containing double and single-stranded DNA with a combined average length of 2600 nucleotides. L...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Lee J,Chastain PD 2nd,Griffith JD,Richardson CC

    更新日期:2002-02-08 00:00:00

  • Direct visualisation of conformational changes in EF(0)F(1) by electron microscopy.

    abstract::The isolated H(+)-ATPase from Escherichia coli (EF(0)F(1)) was investigated by electron microscopy of samples of negatively stained monodisperse molecules, followed by single-particle image processing. The resulting three-dimensional maps showed that the F(1)-part is connected by a prominent stalk to a more peripheral...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Böttcher B,Bertsche I,Reuter R,Gräber P

    更新日期:2000-02-18 00:00:00

  • On the role of alphaThr183 in the allosteric regulation and catalytic mechanism of tryptophan synthase.

    abstract::The catalytic activity and substrate channeling of the pyridoxal 5'-phosphate-dependent tryptophan synthase alpha(2)beta(2) complex is regulated by allosteric interactions that modulate the switching of the enzyme between open, low activity and closed, high activity states during the catalytic cycle. The highly conser...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Kulik V,Weyand M,Seidel R,Niks D,Arac D,Dunn MF,Schlichting I

    更新日期:2002-12-06 00:00:00

  • The immunoglobulin-like domains 1 and 2 of the protein tyrosine phosphatase LAR adopt an unusual horseshoe-like conformation.

    abstract::Neurogenesis depends on exquisitely regulated interactions between macromolecules on the cell surface and in the extracellular matrix. In particular, interactions between proteoglycans and members of the type IIa subgroup of receptor protein tyrosine phosphatases underlie crucial developmental processes such as the fo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Biersmith BH,Hammel M,Geisbrecht ER,Bouyain S

    更新日期:2011-05-13 00:00:00

  • Crystallization of complexes of EcoRV endonuclease with cognate and non-cognate DNA fragments.

    abstract::Complexes of the type II restriction endonuclease EcoRV with a variety of short, selfcomplementary deoxyoligonucleotides have been crystallized. The best crystals diffract to about 2.7 A resolution and consist of 1:1 complexes between endonuclease dimers and duplexes of the cognate decamer GGGATATCCC containing the he...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Winkler FK,D'Arcy A,Blöcker H,Frank R,van Boom JH

    更新日期:1991-01-20 00:00:00

  • Dissecting the Conformational Dynamics of the Bile Acid Transporter Homologue ASBTNM.

    abstract::Apical sodium-dependent bile acid transporter (ASBT) catalyses uphill transport of bile acids using the electrochemical gradient of Na+ as the driving force. The crystal structures of two bacterial homologues ASBTNM and ASBTYf have previously been determined, with the former showing an inward-facing conformation, and ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Lu PH,Li CC,Chiang YW,Liu JH,Chiang WT,Chao YH,Li GS,Weng SE,Lin SY,Hu NJ

    更新日期:2021-01-13 00:00:00

  • Formation and seeding of amyloid fibrils from wild-type hen lysozyme and a peptide fragment from the beta-domain.

    abstract::Wild-type hen lysozyme has been converted from its soluble native state into highly organized amyloid fibrils. In order to achieve this conversion, conditions were chosen to promote partial unfolding of the native globular fold and included heating of low-pH solutions and addition of organic solvents. Two peptides der...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Krebs MR,Wilkins DK,Chung EW,Pitkeathly MC,Chamberlain AK,Zurdo J,Robinson CV,Dobson CM

    更新日期:2000-07-14 00:00:00

  • Amplification of distinct subfamilies of short interspersed elements during evolution of the Salmonidae.

    abstract::There are at least three different kinds of short interspersed repetitive elements in salmonid genomes. Of these, members of the HpaI family are found to be most widely distributed in salmonid species. The HpaI family is present with high copy numbers in all members of the subfamily Salmoninae, such as salmon, trout a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Kido Y,Himberg M,Takasaki N,Okada N

    更新日期:1994-09-02 00:00:00

  • Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces.

    abstract::Lactoferrin is an iron transport protein. Upon binding iron, the two domains in the N-terminal half of the molecule move together. Previous work has shown that this domain closure involves two hinges. Using the newly refined structure of the open form, the structural mechanism underlying this motion is analyzed here i...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Gerstein M,Anderson BF,Norris GE,Baker EN,Lesk AM,Chothia C

    更新日期:1993-11-20 00:00:00

  • Crystal structure of muconate lactonizing enzyme at 3 A resolution.

    abstract::The crystal structure of muconate lactonizing enzyme has been solved at 3 A resolution, and an unambiguous alpha-carbon backbone chain trace made. The enzyme contains three domains; the central domain is a parallel-stranded alpha-beta barrel, which has previously been reported in six other enzymes, including triose ph...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Goldman A,Ollis DL,Steitz TA

    更新日期:1987-03-05 00:00:00

  • Crystal and molecular structure of human annexin V after refinement. Implications for structure, membrane binding and ion channel formation of the annexin family of proteins.

    abstract::Two crystal forms (P6(3) and R3) of human annexin V have been crystallographically refined at 2.3 A and 2.0 A resolution to R-values of 0.184 and 0.174, respectively, applying very tight stereochemical restraints with deviations from ideal geometry of 0.01 A and 2 degrees. The three independent molecules (2 in P6(3), ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Huber R,Berendes R,Burger A,Schneider M,Karshikov A,Luecke H,Römisch J,Paques E

    更新日期:1992-02-05 00:00:00

  • Atomic-Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N-Terminal Domain.

    abstract::Many essential biological processes are mediated by complex molecular machines comprising multiple subunits. Knowledge on the architecture of individual subunits and their positions within the overall multimeric complex is key to understanding the molecular mechanisms of macromolecular assemblies. The anaphase-promoti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Cronin NB,Yang J,Zhang Z,Kulkarni K,Chang L,Yamano H,Barford D

    更新日期:2015-10-09 00:00:00

  • High-resolution crystal structures of trimeric and rod phycocyanin.

    abstract::The phycobilisome light-harvesting antenna in cyanobacteria and red algae is assembled from two substructures: a central core composed of allophycocyanin surrounded by rods that always contain phycocyanin (PC). Unpigmented proteins called linkers are also found within the rods and core. We present here two new structu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: David L,Marx A,Adir N

    更新日期:2011-01-07 00:00:00