A New Type of Circular RNA derived from Nonconventional Introns in Nuclear Genes of Euglenids.

Abstract:

:Nuclear protein-coding genes of euglenids (Discoba, Euglenozoa, Euglenida) contain conventional (spliceosomal) and nonconventional introns. The latter have been found only in euglenozoans. A unique feature of nonconventional introns is the ability to form a stable and slightly conserved RNA secondary structure bringing together intron ends and placing adjacent exons in proximity. To date, little is known about the mechanism of their excision (e.g. whether it involves the spliceosome or not). The tubA gene of Euglena gracilis harbors three conventional and three nonconventional introns. While the conventional introns are excised as lariats, nonconventional introns are present in the cell solely as circular RNAs with full-length ends. Based on this discovery as well as on previous observations indicating that nonconventional introns are observed frequently at unique positions of genes, we suggest that this new type of intronic circRNA might play a role in intron mobility.

journal_name

J Mol Biol

authors

Gumińska N,Zakryś B,Milanowski R

doi

10.1016/j.jmb.2020.166758

subject

Has Abstract

pub_date

2021-02-05 00:00:00

pages

166758

issue

3

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(20)30683-5

journal_volume

433

pub_type

杂志文章
  • Cooperative effects of cofilin (ADF) on actin structure suggest allosteric mechanism of cofilin function.

    abstract::Using site-specific fluorescence probes and cross-linking we demonstrated that cofilin (ADF), a key regulator of actin cellular dynamics, weakens longitudinal contacts in F-actin in a cooperative manner. Differential scanning calorimetry detected a dual nature of cofilin effects on F-actin conformation. At sub-stoichi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.11.072

    authors: Bobkov AA,Muhlrad A,Pavlov DA,Kokabi K,Yilmaz A,Reisler E

    更新日期:2006-02-17 00:00:00

  • A clathrin, caveolae, and dynamin-independent endocytic pathway requiring free membrane cholesterol drives HIV-1 internalization and infection in polarized trophoblastic cells.

    abstract::In human trophoblastic cells, a correlation between early endosomal trafficking of HIV-1 and virus infection was previously documented. However, if HIV-1 is massively internalized in these cells, the endocytic pathway(s) responsible for viral uptake is still undefined. Here we address this vital question. Amongst all ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.03.003

    authors: Vidricaire G,Tremblay MJ

    更新日期:2007-05-18 00:00:00

  • Short peptides act as inducers, anti-inducers and corepressors of Tet repressor.

    abstract::Protein allostery plays a pivotal role in many regulatory processes. Prominent examples are cell-surface receptors, which allosterically transmit ligand-generated signals to their cytoplasmic domains, or bacterial transcription factors, which alternate between a free conformation and a DNA-bound conformation in respon...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.12.009

    authors: Goeke D,Kaspar D,Stoeckle C,Grubmüller S,Berens C,Klotzsche M,Hillen W

    更新日期:2012-02-10 00:00:00

  • Unidirectional replication as visualized by two-dimensional agarose gel electrophoresis.

    abstract::Two-dimensional (2D) agarose gel electrophoresis is progressively replacing electron microscopy as the technique of choice to map the initiation and termination sites for DNA replication. Two different versions were originally developed to analyze the replication of the yeast 2 microns plasmid. Neutral/Neutral (N/N) 2...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90357-c

    authors: Martín-Parras L,Hernández P,Martínez-Robles ML,Schvartzman JB

    更新日期:1991-08-20 00:00:00

  • Cooperative unfolding of a metastable serpin to a molten globule suggests a link between functional and folding energy landscapes.

    abstract::Alpha-1 antitrypsin (alpha(1)-AT) is a member of the serpin class of protease inhibitors, and folds to a metastable state rather than its thermodynamically most stable native state. Upon cleavage by a target protease, alpha(1)-AT undergoes a dramatic conformational change to a stable form, translocating the bound prot...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.05.039

    authors: Tsutsui Y,Wintrode PL

    更新日期:2007-08-03 00:00:00

  • The LcrG Tip Chaperone Protein of the Yersinia pestis Type III Secretion System Is Partially Folded.

    abstract::The type III secretion system (T3SS) is essential in the pathogenesis of Yersinia pestis, the causative agent of plague. A small protein, LcrG, functions as a chaperone to the tip protein LcrV, and the LcrG-LcrV interaction is important in regulating protein secretion through the T3SS. The atomic structure of the LcrG...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2015.07.024

    authors: Chaudhury S,de Azevedo Souza C,Plano GV,De Guzman RN

    更新日期:2015-09-25 00:00:00

  • Structural plasticity of the nuclear pore complex.

    abstract::The nuclear pore complex (NPC) is strategically located at continuous junctions of the inner and outer nuclear membranes to catalyze macromolecular transport, without impending the diffusion of small molecules. In this paper, the structural plasticity of 4412 NPCs in isolated nuclear envelopes has been evaluated, util...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(95)80050-6

    authors: Akey CW

    更新日期:1995-04-28 00:00:00

  • Crystal structure of the Drosophila peptidoglycan recognition protein (PGRP)-SA at 1.56 A resolution.

    abstract::Peptidoglycan recognition proteins (PGRPs) form a recently discovered protein family, which is conserved from insect to mammals and is implicated in the innate immune system by interacting with/or degrading microbial peptidoglycans (PGNs). Drosophila PGRP-SA is a member of this family of pattern recognition receptors ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.04.077

    authors: Reiser JB,Teyton L,Wilson IA

    更新日期:2004-07-16 00:00:00

  • A second higher vertebrate B-type lamin. cDNA sequence determination and in vitro processing of chicken lamin B2.

    abstract::The chicken nuclear lamina is composed of at least three proteins called lamins A, B1 and B2. In addition, putative precursors are transiently expressed during in vivo synthesis of lamins A and B2. Here we report the complete sequence of lamin B2 as it is deduced from a cloned cDNA. Comparison of lamin B2 with lamins ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90505-6

    authors: Vorburger K,Lehner CF,Kitten GT,Eppenberger HM,Nigg EA

    更新日期:1989-08-05 00:00:00

  • From adenylate cyclase to guanylate cyclase. Mutational analysis of a change in substrate specificity.

    abstract::Adenylate and guanylate cyclases, having different but related substrates, are a paradigm for the study of substrate discrimination. A prokaryotic adenylate cyclase gene, phylogenetically related to eukaryotic counterparts, was screened for mutants remodelling the enzyme's specificity. In a first step, a mutant was se...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90093-y

    authors: Beuve A,Danchin A

    更新日期:1992-06-20 00:00:00

  • The effect of chloramphenicol in intact erythroid cells.

    abstract::Incubation of intact reticulocytes with chloramphenicol at concentrations over 10(-3) M caused inhibition of protein synthesis and conversion of polyribosomes to single ribosomes. At 3 x 10(-3) M-chloramphenicol these effects were completely reversible, but reversibility decreased as the chloramphenicol concentration ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(66)90026-x

    authors: Godchaux W 3rd,Herbert E

    更新日期:1966-11-28 00:00:00

  • Regulation of UvrD Helicase Activity by MutL.

    abstract::Escherichia coli UvrD is a superfamily 1 helicase/translocase involved in multiple DNA metabolic processes including methyl-directed mismatch DNA repair. Although a UvrD monomer can translocate along single-stranded DNA, a UvrD dimer is needed for processive helicase activity in vitro. E. coli MutL, a regulatory prote...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2018.08.022

    authors: Ordabayev YA,Nguyen B,Niedziela-Majka A,Lohman TM

    更新日期:2018-10-19 00:00:00

  • Characterization of a conserved alpha-helical, coiled-coil motif at the C-terminal domain of the ATP-dependent FtsH (HflB) protease of Escherichia coli.

    abstract::FtsH (HflB) is an ATP-dependent protease found in prokaryotic cells, mitochondria and chloroplasts. Here, we have identified, in the carboxy-terminal region of FtsH (HfIB), a short alpha helix predicted of forming a coiled-coil, leucine zipper, structure. This region appears to be structurally conserved. The presence ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3767

    authors: Shotland Y,Teff D,Koby S,Kobiler O,Oppenheim AB

    更新日期:2000-06-16 00:00:00

  • Local encoding of computationally designed enzyme activity.

    abstract::One aim of computational protein design is to introduce novel enzyme activity into proteins of known structure by predicting mutations that stabilize transition states. Previously, we showed that it is possible to introduce triose phosphate isomerase activity into the ribose-binding protein of Escherichia coli by cons...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.12.002

    authors: Allert M,Dwyer MA,Hellinga HW

    更新日期:2007-02-23 00:00:00

  • Complete assignment of the 1H nuclear magnetic resonance spectrum of French bean plastocyanin. Sequential resonance assignments, secondary structure and global fold.

    abstract::Sequence-specific proton nuclear magnetic resonance (n.m.r.) assignments for all 99 amino acid residues of French bean Cu(I) plastocyanin are described. The assignments were made using standard sequential assignment procedures and were greatly facilitated by the availability of complete spin system assignments. The ch...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90291-4

    authors: Chazin WJ,Wright PE

    更新日期:1988-08-05 00:00:00

  • Structural comparisons of some small spherical plant viruses.

    abstract::The structures of tomato bushy stunt virus, southern bean mosaic virus and satellite tobacco necrosis virus have been compared quantitatively. The organization of the shell domains of tomato bushy stunt virus and southern bean mosaic virus within the icosahedral envelope is identical. The wedge-shaped end of the subun...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80276-9

    authors: Rossmann MG,Abad-Zapatero C,Murthy MR,Liljas L,Jones TA,Strandberg B

    更新日期:1983-04-25 00:00:00

  • Mapping the Allosteric Communication Network of Aminodeoxychorismate Synthase.

    abstract::Allosteric communication between different subunits in metabolic enzyme complexes is of utmost physiological importance but only understood for few systems. We analyzed the structural basis of allostery in aminodeoxychorismate synthase (ADCS), which is a member of the family of glutamine amidotransferases and catalyze...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2019.05.021

    authors: Semmelmann F,Straub K,Nazet J,Rajendran C,Merkl R,Sterner R

    更新日期:2019-07-12 00:00:00

  • Bacterial comparative genomic hybridization: a method for directly identifying lateral gene transfer.

    abstract::Horizontally transferred DNA is largely responsible for the dissemination of virulence traits amongst bacteria. Rapid identification of acquired DNA remains difficult as whole-genome sequencing of outbreak strains is impractical, and microarray-based approaches, while powerful, are limited to genes present only in the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4925

    authors: Malloff CA,Fernandez RC,Lam WL

    更新日期:2001-09-07 00:00:00

  • Novel inhibitor for prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis and details of substrate-recognition mechanism.

    abstract::A new inhibitor, H-Ala-Ile-pyrrolidin-2-yl boronic acid, was developed as an inhibitor against prolyl tripeptidyl aminopeptidase with a K(i) value of 88.1 nM. The structure of the prolyl tripeptidyl aminopeptidase complexed with the inhibitor (enzyme-inhibitor complex) was determined at 2.2 A resolution. The inhibitor...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.09.077

    authors: Xu Y,Nakajima Y,Ito K,Zheng H,Oyama H,Heiser U,Hoffmann T,Gärtner UT,Demuth HU,Yoshimoto T

    更新日期:2008-01-18 00:00:00

  • Mannan-binding lectin: structure, oligomerization, and flexibility studied by atomic force microscopy.

    abstract::Mannan-binding lectin (MBL) is the archetypical pathogen recognition molecule of the innate immune defense. Upon binding to microorganisms, reactions leading to the destruction of the offender ensue. MBL is an oligomer of structural subunits each composed of three identical polypeptides. We used atomic force microscop...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.05.083

    authors: Jensenius H,Klein DC,van Hecke M,Oosterkamp TH,Schmidt T,Jensenius JC

    更新日期:2009-08-07 00:00:00

  • Action at hooked or twisted-hooked DNA juxtapositions rationalizes unlinking preference of type-2 topoisomerases.

    abstract::The mathematical basis of the hypothesis that type-2 topoisomerases recognize and act at specific DNA juxtapositions has been investigated by coarse-grained lattice polymer models, showing that selective segment passages at hooked juxtapositions can result in dramatic reductions in catenane and knot populations. The l...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.05.007

    authors: Liu Z,Zechiedrich L,Chan HS

    更新日期:2010-07-30 00:00:00

  • E. coli RpsO mRNA decay: RNase E processing at the beginning of the coding sequence stimulates poly(A)-dependent degradation of the mRNA.

    abstract::The rpsO mRNA of E. coli encoding ribosomal protein S15 is destabilized by poly(A) tails posttranscriptionally added by poly(A)polymerase I. We demonstrate here that polyadenylation also contributes to the rapid degradation of mRNA fragments generated by RNase E. It was already known that an RNase E cleavage occurring...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2547

    authors: Hajnsdorf E,Régnier P

    更新日期:1999-03-05 00:00:00

  • Insights into strand exchange in BTB domain dimers from the crystal structures of FAZF and Miz1.

    abstract::The BTB domain is a widely distributed protein-protein interaction motif that is often found at the N-terminus of zinc finger transcription factors. Previous crystal structures of BTB domains have revealed tightly interwound homodimers, with the N-terminus from one chain forming a two-stranded anti-parallel beta-sheet...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.05.028

    authors: Stogios PJ,Cuesta-Seijo JA,Chen L,Pomroy NC,Privé GG

    更新日期:2010-07-30 00:00:00

  • Constraining enzyme conformational change by an antibody leads to hyperbolic inhibition.

    abstract::Although it has been known for many years that antibodies display properties characteristic of allosteric effectors, the molecular mechanisms responsible for these effects remain poorly understood. Here, we describe a single-domain antibody fragment (nanobody) that modulates protein function by constraining conformati...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.01.017

    authors: Oyen D,Srinivasan V,Steyaert J,Barlow JN

    更新日期:2011-03-18 00:00:00

  • Minimum-energy path for a u6 RNA conformational change involving protonation, base-pair rearrangement and base flipping.

    abstract::The U6 RNA internal stem-loop (U6 ISL) is a highly conserved domain of the spliceosome that is important for pre-mRNA splicing. The U6 ISL contains an internal loop that is in equilibrium between two conformations controlled by the protonation state of an adenine (pK(a)=6.5). Lower pH favors formation of a protonated ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.07.003

    authors: Venditti V,Clos L 2nd,Niccolai N,Butcher SE

    更新日期:2009-09-04 00:00:00

  • Contribution of opening and bending dynamics to specific recognition of DNA damage.

    abstract::Guanine-uracil (G.U) wobble base-pairs are a detrimental lesion in DNA. Previous investigations have shown that such wobble base-pairs are more prone to base-opening than the normal G.C base-pairs. To investigate the sequence-dependence of base-pair opening we have performed 5ns molecular dynamics simulations on G.U w...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00598-9

    authors: Seibert E,Ross JB,Osman R

    更新日期:2003-07-18 00:00:00

  • Expanding the Paradigm: Intrinsically Disordered Proteins and Allosteric Regulation.

    abstract::Allosteric regulatory processes are implicated at all levels of biological function. Recent advances in our understanding of the diverse and functionally significant class of intrinsically disordered proteins have identified a multitude of ways in which disordered proteins function within the confines of the allosteri...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2018.04.003

    authors: Berlow RB,Dyson HJ,Wright PE

    更新日期:2018-08-03 00:00:00

  • Ketoconazole-induced conformational changes in the active site of cytochrome P450eryF.

    abstract::The azole-based P450 inhibitor ketoconazole is used to treat fungal infections and functions by blocking ergosterol biosynthesis in yeast. Ketoconazole binds to mammalian P450 enzymes and this can result in drug-drug interactions and lead to liver damage. To identify protein-drug interactions that contribute to bindin...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4803

    authors: Cupp-Vickery JR,Garcia C,Hofacre A,McGee-Estrada K

    更新日期:2001-08-03 00:00:00

  • High-resolution structure of bovine pancreatic trypsin inhibitor with altered binding loop sequence.

    abstract::A mutant of bovine pancreatic trypsin inhibitor (BPTI) has been constructed and expressed in Escherichia coli in order to probe the kinetic and structural consequences of truncating the binding loop residues to alanine. In addition to two such mutations (Thr11Ala and Pro13Ala), it has a conservative Lys15Arg substitut...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3445

    authors: Czapinska H,Otlewski J,Krzywda S,Sheldrick GM,Jaskólski M

    更新日期:2000-02-04 00:00:00

  • Calcium binding sites in tomato bushy stunt virus visualized by Laue crystallography.

    abstract::We have collected Laue diffraction data from crystals of tomato bushy stunt virus using the full white X-ray spectrum from the wiggler magnet of the Synchrotron Radiation Source at Daresbury, U.K. A single 24 second exposure of a crystal soaked in EDTA yielded a data set that was 90% complete between 6 and 3.5 A resol...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(90)90278-T

    authors: Campbell JW,Clifton IJ,Greenhough TJ,Hajdu J,Harrison SC,Liddington RC,Shrive AK

    更新日期:1990-08-05 00:00:00