当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Amplification of distinct subfamilies of short interspersed elements during evolution of the Salmonidae.

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 and charr. In order to determine whether the amplification of the Hpa sequence occurred rapidly within a short evolutionary period or gradually, over the long term, a search was made for Hpa sequences in primitive salmonids; namely, grayling and whitefish. A grayling species has fivefold fewer copies of these sequences than the Salmoninae species, whereas several whitefish species have 200-fold to 20-fold fewer copies than the Salmoniae species. Characterization of the Hpa sequences in these species allowed us to recognize two distinct Hpa subfamilies on the basis of diagnostic substitutions as well as a new short interspersed element with an Hpa-related sequence. The distribution of these sequences revealed that distinct members of the HpaI or Hpa-related family were amplified during establishment of each subfamily lineage in a manner very similar to the amplification of the human Alu family. We provide evidence for the validity of a model that involves "multiple source genes" to explain diagnostic substitutions of the Hpa subfamilies and the timing of their appearance during evolution.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Kido Y,Himberg M,Takasaki N,Okada N

doi

10.1006/jmbi.1994.1540

subject

Has Abstract

pub_date

1994-09-02 00:00:00

pages

633-44

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(84)71540-3

journal_volume

241

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Time to be versatile: regulation of the replication timing program in budding yeast.

    abstract：:Eukaryotic replication origins are activated at different times during the S phase of the cell cycle, following a temporal program that is stably transmitted to daughter cells. Although the mechanisms that control initiation at the level of individual origins are now well understood, much less is known on how cells co...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2013.09.020

    authors： Yoshida K,Poveda A,Pasero P

    更新日期：2013-11-29 00:00:00

  • Sub-atomic resolution crystal structure of cholesterol oxidase: what atomic resolution crystallography reveals about enzyme mechanism and the role of the FAD cofactor in redox activity.

    abstract：:The crystal structure of cholesterol oxidase, a 56kDa flavoenzyme was anisotropically refined to 0.95A resolution. The final crystallographic R-factor and R(free) value is 11.0% and 13.2%, respectively. The quality of the electron density maps has enabled modeling of alternate conformations for 83 residues in the enzy...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00054-8

    authors： Lario PI,Sampson N,Vrielink A

    更新日期：2003-03-07 00:00:00

  • Evolution of stability in a cold-active enzyme elicits specificity relaxation and highlights substrate-related effects on temperature adaptation.

    abstract：:Molecular aspects of thermal adaptation of proteins were studied by following the co-evolution of temperature dependence, conformational stability, and substrate specificity in a cold-active lipase modified via directed evolution. We found that the evolution of kinetic stability was accompanied by a relaxation in subs...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.10.026

    authors： Gatti-Lafranconi P,Natalello A,Rehm S,Doglia SM,Pleiss J,Lotti M

    更新日期：2010-01-08 00:00:00

  • SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family.

    abstract：:We have developed a procedure to predict the peptide binding specificity of an SH3 domain from its sequence. The procedure utilizes information extracted from position-specific contacts derived from six SH3/peptide or SH3/protein complexes of known structure. The framework of SH3/peptide contacts defined on the struct...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3670

    authors： Brannetti B,Via A,Cestra G,Cesareni G,Helmer-Citterich M

    更新日期：2000-04-28 00:00:00

  • Mitochondrial respiratory chain supercomplexes are destabilized in Barth Syndrome patients.

    abstract：:Mutations in the human TAZ gene are associated with Barth Syndrome, an often fatal X-linked disorder that presents with cardiomyopathy and neutropenia. The TAZ gene encodes Tafazzin, a putative phospholipid acyltranferase that is involved in the remodeling of cardiolipin, a phospholipid unique to the inner mitochondri...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.06.057

    authors： McKenzie M,Lazarou M,Thorburn DR,Ryan MT

    更新日期：2006-08-18 00:00:00

  • The Spliceosomal Protein SF3B5 is a Novel Component of Drosophila SAGA that Functions in Gene Expression Independent of Splicing.

    abstract：:The interaction between splicing factors and the transcriptional machinery provides an intriguing link between the coupled processes of transcription and splicing. Here, we show that the two components of the SF3B complex, SF3B3 and SF3B5, that form part of the U2 small nuclear ribonucleoprotein particle (snRNP) are a...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2016.05.009

    authors： Stegeman R,Spreacker PJ,Swanson SK,Stephenson R,Florens L,Washburn MP,Weake VM

    更新日期：2016-09-11 00:00:00

  • Nuclear transport of Ras-associated tumor suppressor proteins: different transport receptor binding specificities for arginine-rich nuclear targeting signals.

    abstract：:Ras proteins regulate a wide range of biological processes by interacting with a variety of effector proteins. In addition to the known role in tumorigensis, the activated form of Ras exhibits growth-inhibitory effects by unknown mechanisms. Several Ras effector proteins identified as mediators of apoptosis and cell-c...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.01.026

    authors： Kumari G,Singhal PK,Rao MR,Mahalingam S

    更新日期：2007-04-13 00:00:00

  • Interaction of the Dengue virus fusion peptide with membranes assessed by NMR: The essential role of the envelope protein Trp101 for membrane fusion.

    abstract：:Dengue virus (DV) infection depends on a step of membrane fusion, which occurs in the acidic environment of the endosome. This process is mediated by virus surface envelope glycoprotein, in which the loop between residues D98-G112 is considered to be crucial, acting as a fusion peptide. Here, we have characterized fun...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.07.035

    authors： Melo MN,Sousa FJ,Carneiro FA,Castanho MA,Valente AP,Almeida FC,Da Poian AT,Mohana-Borges R

    更新日期：2009-09-25 00:00:00

  • Shaping the Immune Landscape in Cancer by Galectin-Driven Regulatory Pathways.

    abstract：:Along with the discovery of tumor-driven inflammatory pathways, there has been a considerable progress over the past 10years in understanding the mechanisms leading to cancer immunosurveillance and immunoediting. Several regulatory pathways, typically involved in immune cell homeostasis, are co-opted by cancer cells t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2016.03.021

    authors： Rabinovich GA,Conejo-García JR

    更新日期：2016-08-14 00:00:00

  • Mutations upstream of the ribosome-binding site affect translational efficiency.

    abstract：:The DNA coding for the major outer membrane lipoprotein of Escherichia coli has been fused to the coding region of the beta-galactosidase gene to measure the effect of various mutations on the efficiency of translation initiation. The various mutants were made by either inserting or deleting a small number of nucleoti...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(85)90332-8

    authors： Coleman J,Inouye M,Nakamura K

    更新日期：1985-01-05 00:00:00

  • Role of structural and dynamical plasticity in Sin3: the free PAH2 domain is a folded module in mSin3B.

    abstract：:The co-repressor Sin3 is the essential scaffold protein of the Sin3/HDAC co-repressor complex, which is recruited to the DNA by a diverse group of transcriptional repressors, targeting genes involved in the regulation of the cell cycle, proliferation and differentiation. Sin3 contains four repeats commonly denoted as ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.01.100

    authors： van Ingen H,Baltussen MA,Aelen J,Vuister GW

    更新日期：2006-04-28 00:00:00

  • Modular structure of the trigger factor required for high activity in protein folding.

    abstract：:The Escherichia coli trigger factor is a peptidyl-prolyl cis/trans isomerase (PPIase) which catalyzes proline-limited protein folding extremely well. It has been found associated with nascent protein chains as well as with the chaperone GroEL. The trigger factor utilizes protein regions outside the central catalytic d...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1206

    authors： Zarnt T,Tradler T,Stoller G,Scholz C,Schmid FX,Fischer G

    更新日期：1997-09-05 00:00:00

  • Functional and structural role of amino acid residues in the odd-numbered transmembrane alpha-helices of the bovine mitochondrial oxoglutarate carrier.

    abstract：:The mitochondrial oxoglutarate carrier (OGC) plays an important role in the malate-aspartate shuttle, the oxoglutarate-isocitrate shuttle and gluconeogenesis. To establish amino acid residues that are important for function, each residue in the transmembrane alpha-helices H1, H3 and H5 was replaced systematically by a...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.03.048

    authors： Cappello AR,Miniero DV,Curcio R,Ludovico A,Daddabbo L,Stipani I,Robinson AJ,Kunji ER,Palmieri F

    更新日期：2007-06-01 00:00:00

  • The crystal structure of affinity-matured human growth hormone at 2 A resolution.

    abstract：:A variant of human growth hormone (hGH), in which 15 mutations were introduced with phage display mutagenesis to improve receptor binding affinity by 400-fold, yielded two related crystal forms diffracting to high resolution. The structure of this variant was determined in both crystal forms, one at 2.0 A resolution a...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1135

    authors： Ultsch MH,Somers W,Kossiakoff AA,de Vos AM

    更新日期：1994-02-11 00:00:00

  • Associative and structural properties of the region of complement factor H encompassing the Tyr402His disease-related polymorphism and its interactions with heparin.

    abstract：:Factor H (FH) is a major complement control protein in serum. The seventh short complement regulator (SCR-7) domain of the 20 in FH is associated with age-related macular degeneration through a Tyr402His polymorphism. The recombinant SCR-6/8 domains containing either His402 or Tyr402 and their complexes with a heparin...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.02.038

    authors： Fernando AN,Furtado PB,Clark SJ,Gilbert HE,Day AJ,Sim RB,Perkins SJ

    更新日期：2007-04-27 00:00:00

  • A distal, high-affinity binding site on the cyclin-CDK substrate Pho4 is important for its phosphorylation and regulation.

    abstract：:Cyclins and cyclin-dependent kinases (CDKs) are key components of signaling pathways essential for cell growth and survival. The cyclin-CDK Pho80-Pho85 inactivates the transcription factor Pho4 in budding yeast by phosphorylating it on five sites. We isolated seven single amino acid substitutions outside of the phosph...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2003.10.035

    authors： Byrne M,Miller N,Springer M,O'Shea EK

    更新日期：2004-01-02 00:00:00

  • Structural and biophysical characterization of the Syk activation switch.

    abstract：:Syk is an essential non-receptor tyrosine kinase in intracellular immunological signaling, and the control of Syk kinase function is considered as a valuable target for pharmacological intervention in autoimmune or inflammation diseases. Upon immune receptor stimulation, the kinase activity of Syk is regulated by bind...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2012.11.007

    authors： Grädler U,Schwarz D,Dresing V,Musil D,Bomke J,Frech M,Greiner H,Jäkel S,Rysiok T,Müller-Pompalla D,Wegener A

    更新日期：2013-01-23 00:00:00

  • How Widespread is Metabolite Sensing by Ribosome-Arresting Nascent Peptides?

    abstract：:In order to colonize a niche and compete for scarce resources, microorganisms have evolved means to adjust the expression levels of their biosynthetic enzymes in response to the changing levels of metabolites available to them. To do so, they often rely on transcription factors or structured RNAs that directly sense t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2016.04.019

    authors： Seip B,Innis CA

    更新日期：2016-05-22 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

  • Intracellular antibody capture technology: application to selection of intracellular antibodies recognising the BCR-ABL oncogenic protein.

    abstract：:The expression of antibodies inside cells to ablate protein function has the potential for disease therapy and for target validation in functional genomics. However, due to inefficient expression or folding, only a few antibodies or antibody fragments, usually as single-chain Fv antibody fragments (scFv), bind their a...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2002.5403

    authors： Tse E,Lobato MN,Forster A,Tanaka T,Chung GT,Rabbitts TH

    更新日期：2002-03-15 00:00:00

  • Mutant p53 in Cancer: Accumulation, Gain-of-Function, and Therapy.

    abstract：:Tumor suppressor p53 plays a central role in tumor suppression. p53 is the most frequently mutated gene in human cancer, and over half of human cancers contain p53 mutations. Majority of p53 mutations in cancer are missense mutations, leading to the expression of full-length mutant p53 (mutp53) protein. While the crit...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2017.03.030

    authors： Yue X,Zhao Y,Xu Y,Zheng M,Feng Z,Hu W

    更新日期：2017-06-02 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

  • 3D gene of foot-and-mouth disease virus. Conservation by convergence of average sequences.

    abstract：:The nucleotide sequence of the 3D (polymerase) gene of eight epidemiologically related isolates of foot-and-mouth disease virus of serotype C1 is reported. The genetic heterogeneity of 3D RNA is compared with that of the VP1-coding RNA of the same viruses. Regression lines of substitutions per nucleotide that distingu...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90367-1

    authors： Villaverde A,Martínez-Salas E,Domingo E

    更新日期：1988-12-05 00:00:00

  • Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer's Abeta(1-40) peptide.

    abstract：:We use a coarse-grained protein model to characterize the critical nucleus, structural stability, and fibril elongation propensity of Abeta(1-40) oligomers for the C(2x) and C(2z) quaternary forms proposed by solid-state NMR. By estimating equilibrium populations of structurally stable and unstable protofibrils, we de...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.10.011

    authors： Fawzi NL,Okabe Y,Yap EH,Head-Gordon T

    更新日期：2007-01-12 00:00:00

  • Decay of rplN and lacZ mRNA in Escherichia coli.

    abstract：:To examine the previously proposed retroregulation model of spc mRNA degradation, two strains of Escherichia coli B/r were used; one has wild-type spc and lac operons and the other has a lac operon deletion, a wild-type spc operon, and a Pspc-rplN-lacZ fusion operon lacking the normal control sites of the spc operon (...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2710

    authors： Liang ST,Ehrenberg M,Dennis P,Bremer H

    更新日期：1999-05-14 00:00:00

  • Crystal structures of the complexes between vancomycin and cell-wall precursor analogs.

    abstract：:The crystal structures of three vancomycin complexes with two vancomycin-sensitive cell-wall precursor analogs (diacetyl-Lys-D-Ala-D-Ala and acetyl-D-Ala-D-Ala) and a vancomycin-resistant cell-wall precursor analog (diacetyl-Lys-D-Ala-D-lactate) were determined at atomic resolutions of 1.80 A, 1.07 A, and 0.93 A, resp...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.10.026

    authors： Nitanai Y,Kikuchi T,Kakoi K,Hanamaki S,Fujisawa I,Aoki K

    更新日期：2009-02-06 00:00:00

  • The remarkable mechanical strength of polycystin-1 supports a direct role in mechanotransduction.

    abstract：:Polycystin-1 is a large membrane-associated protein that interacts with polycystin-2 in the primary cilia of renal epithelial cells to form a mechanosensitive ion channel. Bending of the cilia induces calcium flow into the cells, mediated by the polycystin complex. Antibodies to polycystin-1 and polycystin-2 abolish t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.04.008

    authors： Forman JR,Qamar S,Paci E,Sandford RN,Clarke J

    更新日期：2005-06-17 00:00:00

  • The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes.

    abstract：:Structure determination of complex molecular machines requires a combination of an increasing number of experimental methods with highly specialized software geared toward each data source to properly handle the gathered data. Recently, we introduced the two software packages PowerFit and DisVis. These combine high-re...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2016.11.032

    authors： van Zundert GC,Trellet M,Schaarschmidt J,Kurkcuoglu Z,David M,Verlato M,Rosato A,Bonvin AM

    更新日期：2017-02-03 00:00:00

  • Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins.

    abstract：:Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small, fast-folding proteins. To investigate the extent of the topological control of the folding process, we studied the folding of simplified models ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3693

    authors： Clementi C,Nymeyer H,Onuchic JN

    更新日期：2000-05-19 00:00:00

  • Analysis of replicative intermediates produced during bacteriophage phi 29 DNA replication in vitro.

    abstract：:Replication of bacteriophage phi 29 DNA initiates at either end of its linear double-stranded DNA molecule and proceeds by a strand-displacement mechanism. In the present paper we have used an in vitro phi 29 DNA replication system to analyse by electron microscopy the replicative intermediates produced at different r...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90589-x

    authors： Gutiérrez C,Sogo JM,Salas M

    更新日期：1991-12-20 00:00:00