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secretory proteins

Overview page. Subjects: Medicine and Health.

A diverse group of proteins, nearly all of which are synthesized on the rough endoplasmic reticulum, cotranslationally transported into the lumen of the endoplasmic reticulum (see signal...

See overview in Oxford Index

Selection for efficient translation initiation biases codon usage at second amino acid position in secretory proteins

Yaramah M. Zalucki, Peter M. Power and Michael P. Jennings.

in Nucleic Acids Research

September 2007; p ublished online August 2007 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4353 words.

The definition of a typical sec-dependent bacterial signal peptide contains a positive charge at the N-terminus, thought to be required for membrane association. In this study the amino...

The C-terminal silencing domain of Rap1p is essential for the repression of ribosomal protein genes in response to a defect in the secretory pathway

Keiko Mizuta, Rota Tsujii, Jonathan R. Warner and Masahiko Nishiyama.

in Nucleic Acids Research

February 1998; p ublished online February 1998 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3923 words.

We have previously shown that a functional secretory pathway is essential for continued ribosome synthesis in Saccharomyces cerevisiae. When a temperaturesensitive mutant defective in the...

Transcription of genes encoding trans‐acting factors required for rRNA maturation/ribosomal subunit assembly is coordinately regulated with ribosomal protein genes and involves Rap1 in Saccharomyces cerevisiae

Keita Miyoshi, Chiharu Shirai and Keiko Mizuta.

in Nucleic Acids Research

April 2003; p ublished online April 2003 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3530 words.

We demonstrate that the genes encoding trans‐ acting factors essential for pre‐rRNA processing/ribosomal subunit assembly are responsive to various kinds of stresses such as heat shock,...

Repression of rRNA synthesis due to a secretory defect requires the C-terminal silencing domain of Rap1p in Saccharomyces cerevisiae

Keita Miyoshi, Tokichi Miyakawa and Keiko Mizuta.

in Nucleic Acids Research

August 2001; p ublished online August 2001 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4468 words.

A secretory defect causes specific transcriptional repression of both ribosomal protein and ribosomal RNA genes, suggesting the coupling of plasma membrane and ribosome syntheses. We...

Engineered viruses to select genes encoding secreted and membrane‐bound proteins in mammalian cells

Pierre Moffatt, Patrick Salois, Marie‐Hélène Gaumond, Natalie St‐Amant, Éric Godin and Christian Lanctôt.

in Nucleic Acids Research

October 2002; p ublished online October 2002 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 7058 words.

We have developed a functional genomics tool to identify the subset of cDNAs encoding secreted and membrane‐bound proteins within a library (the ‘secretome’). A Sindbis virus replicon was...

Signal-exon trap: a novel method for the identification of signal sequences from genomic DNA

Miklós Péterfy, Tibor Gyuris and László Takács.

in Nucleic Acids Research

April 2000; p ublished online April 2000 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5368 words.

We describe a genomic DNA-based signal sequence trap method, signal-exon trap (SET), for the identification of genes encoding secreted and membrane-bound proteins. SET is based on the...

SRPDB (Signal Recognition Particle Database)

Jan Gorodkin, Bjarne Knudsen, Christian Zwieb and Tore Samuelsson.

in Nucleic Acids Research

January 2001; p ublished online January 2001 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 1109 words.

Signal recognition particle (SRP) is a stable cytoplasmic ribonucleoprotein complex that serves to translocate secretory proteins across membranes during translation. The SRP Database...

Identifying secretomes in people, pufferfish and pigs

Eric W. Klee, Daniel F. Carlson, Scott C. Fahrenkrug, Stephen C. Ekker and Lynda B. M. Ellis.

in Nucleic Acids Research

March 2004; p ublished online March 2004 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5283 words.

The proteins processed by the secretory pathway (secretome) are critical players in the development of multi‐cellular eukaryotic organisms but have yet to be comprehensively studied at the...

Regulation of polysome assembly on the endoplasmic reticulum by a coiled-coil protein, p180

Tomonori Ueno, Keiko Kaneko, Tetsutaro Sata, Shunji Hattori and Kiyoko Ogawa-Goto.

in Nucleic Acids Research

April 2012; p ublished online December 2011 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 7505 words.

A coiled-coil microtubule-bundling protein, p180, was originally identified as one of the ribosome receptor candidates on the rough endoplasmic reticulum (ER) and is highly expressed in...

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SEPPA 2.0—more refined server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen

Tao Qi, Tianyi Qiu, Qingchen Zhang, Kailin Tang, Yangyang Fan, Jingxuan Qiu, Dingfeng Wu, Wei Zhang, Yanan Chen, Jun Gao, Ruixin Zhu and Zhiwei Cao.

in Nucleic Acids Research

July 2014; p ublished online May 2014 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 2732 words.

Spatial Epitope Prediction server for Protein Antigens (SEPPA) has received lots of feedback since being published in 2009. In this improved version, relative ASA preference of unit patch...

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A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems

Dapeng Zhang, Lakshminarayan M. Iyer and L. Aravind.

in Nucleic Acids Research

June 2011; p ublished online February 2011 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 14256 words.

The use of nucleases as toxins for defense, offense or addiction of selfish elements is widely encountered across all life forms. Using sensitive sequence profile analysis methods, we...

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Implication of the SMN complex in the biogenesis and steady state level of the Signal Recognition Particle

Nathalie Piazzon, Florence Schlotter, Suzie Lefebvre, Maxime Dodré, Agnès Méreau, Johann Soret, Aurore Besse, Martine Barkats, Rémy Bordonné, Christiane Branlant and Séverine Massenet.

in Nucleic Acids Research

January 2013; p ublished online December 2012 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 11127 words.

Spinal muscular atrophy is a severe motor neuron disease caused by reduced levels of the ubiquitous Survival of MotoNeurons (SMN) protein. SMN is part of a complex that is essential for...

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The tmRDB and SRPDB resources

Ebbe Sloth Andersen, Magnus Alm Rosenblad, Niels Larsen, Jesper Cairo Westergaard, Jody Burks, Iwona K. Wower, Jacek Wower, Jan Gorodkin, Tore Samuelsson and Christian Zwieb.

in Nucleic Acids Research

January 2006; p ublished online January 2006 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5378 words.

Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html with mirror...

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Novel salivary gland specific binding elements located in the PSP proximal enhancer core

Pia Svendsen, Jesper Laursen, Helene Krogh-Pedersen and J. Peter Hjorth.

in Nucleic Acids Research

June 1998; p ublished online June 1998 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 6373 words.

The murine parotid secretory protein (PSP) gene is expressed selectively at high levels in parotid and sublingual salivary glands. Previously, the transcriptional activity of a PSP...

Directed evolution of green fluorescent protein by a new versatile PCR strategy for site-directed and semi-random mutagenesis

Asako Sawano and Atsushi Miyawaki.

in Nucleic Acids Research

August 2000; p ublished online August 2000 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3954 words.

To develop a simple, speedy, economical and widely applicable method for multiple-site mutagenesis, we have substantially modified the Quik-Change™ Site-Directed Mutagenesis Kit protocol...

An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer

Juan Cui, Yunbo Chen, Wen-Chi Chou, Liankun Sun, Li Chen, Jian Suo, Zhaohui Ni, Ming Zhang, Xiaoxia Kong, Lisabeth L. Hoffman, Jinsong Kang, Yingying Su, Victor Olman, Darryl Johnson, Daniel W. Tench, I. Jonathan Amster, Ron Orlando, David Puett, Fan Li and Ying Xu.

in Nucleic Acids Research

March 2011; p ublished online October 2010 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 6800 words.

This report describes an integrated study on identification of potential markers for gastric cancer in patients’ cancer tissues and sera based on: (i) genome-scale transcriptomic analyses...

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Transgene-mediated post-transcriptional gene silencing is inhibited by 3′ non-coding sequences in Paramecium

Angélique Galvani and Linda Sperling.

in Nucleic Acids Research

November 2001; p ublished online November 2001 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 6404 words.

Homology-dependent gene silencing is achieved in Paramecium by introduction of gene coding regions into the somatic nucleus at high copy number, resulting in reduced expression of all...

The brefeldin A resistance protein Bfr1p is a component of polyribosome-associated mRNP complexes in yeast

Brian D. Lang, Ai-min Li, Heather D. Black-Brewster and Judith L. Fridovich-Keil.

in Nucleic Acids Research

June 2001; p ublished online June 2001 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5532 words.

The yeast gene BFR1 was originally isolated from a genetic screen for high-copy suppressors of brefeldin A-induced lethality in Saccharomyces cerevisiae. While this result suggested a...

Characterization of Multigene Families in the Micronuclear Genome of Paramecium Tetraurelia Reveals a Germline Specific Sequence in an Intron of a Centrin Gene

Laurence Vayssié, Linda Sperling and Luisa Madeddu.

in Nucleic Acids Research

March 1997; p ublished online March 1997 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3852 words.

In Paramecium, as in other ciliates, the transcriptionally active macronucleus is derived from the germline micronucleus by programmed DNA rearrangements, which include the precise excision...

Diversity among the primate eosinophil-derived neurotoxin genes: a specific C-terminal sequence is necessary for enhanced ribonuclease activity

Helene F. Rosenberg and Kimberly D. Dyer.

in Nucleic Acids Research

September 1997; p ublished online September 1997 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 2847 words.

The human eosinophil-derived neurotoxin (hEDN) is a secretory effector protein from eosinophilic leukocytes that is a member of the ribonuclease A (RNase A) family of ribonucleases. EDN is...