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The scanning model for translation: an update. (1989)

by M Kozak
Venue:J. Cell Biol.
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Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites

by A. Zien, G. Rätsch, S. Mika, B. Schölkopf, T. Lengauer, K.-R. Müller , 2000
"... Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called translation initiation sites (TIS). Results: The task of finding TIS can be modeled as a classification pro ..."
Abstract - Cited by 133 (14 self) - Add to MetaCart
Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called translation initiation sites (TIS). Results: The task of finding TIS can be modeled as a classification problem. We demonstrate the applicability of support vector machines (SVMs) for this task, and show how to incorporate prior biological knowledge by engineering an appropriate kernel function. With the described techniques the recognition performance can be improved by 26% over leading existing approaches. We provide evidence that existing related methods (e.g. ESTScan) could profit from advanced TIS recognition.

Translation of human hepatitis C virus RNA in cultured cells is mediated by an internal ribosome-binding mechanism

by Changyu Wang, Peter Sarnow, Aleem Siddiqui - J. Virol , 1993
"... The human hepatitis C virus (HCV) contains a long 5 ' noncoding region (5 ' NCR). Computer-assisted and biochemical analyses suggest that there is a complex secondary structure in this region that is comparable to the secondary structures that are found in picornaviruses (E. A. Brown, H. Z ..."
Abstract - Cited by 107 (3 self) - Add to MetaCart
The human hepatitis C virus (HCV) contains a long 5 ' noncoding region (5 ' NCR). Computer-assisted and biochemical analyses suggest that there is a complex secondary structure in this region that is comparable to the secondary structures that are found in picornaviruses (E. A. Brown, H. Zhang, L.-H. Ping, and S. M. Lemon, Nucleic Acids Res. 20:5041-5045, 1992). Previous in vitro studies suggest that the HCV 5 ' NCR plays an important role during translation (K. Tsukiyama-Kohara, N. lizuka, M. Kohara, and A. Nomoto, J. Virol. 66:1476-1483, 1992). Dicistronic and monocistronic expression vectors, in vitro translation, RNA transfec-tions, and deletion mutagenesis studies were utilized to demonstrate unambiguously that the HCV 5 ' NCR is involved in translational control. Our data strongly support the conclusion that an internal ribosome entry site exists within the 5 ' noncoding sequences proximal to the initiator AUG. Furthermore, our results suggest that the HCV genome is translated in a cap-independent manner and that the sequences immediately upstream of the initiator AUG are essential for internal ribosome entry site function during translation. Hepatitis C virus (HCV) is the documented etiologic agent of blood-borne non-A, non-B hepatitis and represents the principal infectious agent associated with posttransfusion hepatitis (4). Recent clinical studies have demonstrated a strong correlation between HCV infection and hepatocellu-lar carcinoma (28). The HCV genome is a single-stranded RNA molecule with plus-strand polarity and is approxi-mately 9,500 nucleotides (nt) long (5, 13, 18, 24, 32). On the basis of sequence comparisons and in vitro translation studies, the HCV genome appears to encode several struc-tural and nonstructural proteins (Fig. 1) (4, 12, 23). This information, in conjunction with additional characteristics, has led to the tentative classification of HCV in the family
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...njunction with additional characteristics, has led to the tentative classification of HCV in the family Flaviviridae (4, 27). Eucaryotic mRNAs are translated by a mechanism known as ribosome scanning =-=(19, 20)-=-. This mechanism involves binding of the 40S ribosomal subunit adjacent to the 5' end of the mRNA, which is mediated by an interaction between the 5' methylated cap structure and the cellular initiati...

Canonical eukaryotic initiation factors determine initiation of translation by internal ribosomal entry

by Tatyana V. Pestova, Christopher U. T. Hellen, Ivan N. Shatsky - Mol. Cell Biol , 1996
"... Translation of picornavirus RNA is initiated after ribosomal binding to an internal ribosomal entry site (IRES) within the 5 * untranslated region.We have reconstituted IRES-mediated initiation on encephalomyocar-ditis virus RNA from purified components and used primer extension analysis to confirm ..."
Abstract - Cited by 106 (25 self) - Add to MetaCart
Translation of picornavirus RNA is initiated after ribosomal binding to an internal ribosomal entry site (IRES) within the 5 * untranslated region.We have reconstituted IRES-mediated initiation on encephalomyocar-ditis virus RNA from purified components and used primer extension analysis to confirm the fidelity of 48S pre-initiation complex formation. Eukaryotic initiation factor 2 (eIF2), eIF3, and eIF4F were required for initiation; eIF4B and to a lesser extent the pyrimidine tract-binding protein stimulated this process. We show that eIF4F binds to the IRES in a novel cap-independent manner and suggest that cap- and IRES-dependent initiation mechanisms utilize different modes of interaction with this factor to promote ribosomal attachment to mRNA. Initiation of eukaryotic protein synthesis is the process of assembly of an 80S initiation complex containing initiator tRNAi Met, 40S, and 60S ribosomal subunits at the initiation codon of an mRNA (42). The first step in this process is formation of a 43S complex that consists of eukaryotic initia-tion factor 2 (eIF2), eIF3, and initiator Met-tRNAi Met bound to
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... several restrictions on the structure of mRNAs that use it: they are capped, have relatively short, unstructured 59 UTRs, and are monocistronic because initiation is limited to the 59-most AUG codon =-=(34)-=-. A second, cap-independent mechanism of ribosome binding is used by mRNAs that contain an internal ribosomal entry site (IRES). IRES-mediated initiation is used by a number of cellular mRNAs, includi...

Functional dissociation of paracellular permeability and transepithelial electrical resistance and disruption of the apical-basolateral intramembrane diffusion barrier by expression of a mutant tight junction membrane protein

by Maria S. Balda, J. Andrew Whitney, Catalina Flores, Marcelino Cereijido, Karl Matter , 1996
"... Abstract. Tight junctions, the most apical of the intercellular junctions that connect individual cells in a epithelial sheet, are thought to form a seal that restricts paracellular and intramembrane diffusion. To analyze the functioning of tight junctions, we generated stable MDCK strain 2 cell lin ..."
Abstract - Cited by 88 (9 self) - Add to MetaCart
Abstract. Tight junctions, the most apical of the intercellular junctions that connect individual cells in a epithelial sheet, are thought to form a seal that restricts paracellular and intramembrane diffusion. To analyze the functioning of tight junctions, we generated stable MDCK strain 2 cell lines expressing either full-length or COOH-terminally truncated chicken occludin, the only known transmembrane component of tight junctions. Confocal immunofluorescence and immunoelectron microscopy demonstrated that mutant occludin was incorporated into tight junctions but, in contrast to full-length chicken occludin, exhibited a discontinuous junctional staining pattern and also disrupted the continuous junctional ring formed by endogenous occludin. This rearrangement of occludin was not paralleled by
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...). HAoecludin and HAoccludinCT3 were generated by PCR using the full-length occludin cDNA as a template. For the NH2-terminal HA epitope a primer was used that contained a KpnI site, Kozak sequences (=-=Kozak, 1989-=-), the HA epitope (MQDLPGNDNSTAGL; Daro et al., 1996), and some nucleotides derived from the 5' end of the coding sequence of occludin (5'-AAAAAGGTACCATGCAGGACCTGCCAGGCAACGACAACAGCACCGCCGGCCTTAAGAAGTC...

Neural Network Prediction of Translation Initiation Sites in Eukaryotes: Perspectives for EST and Genome analysis

by Anders T Gorm Pedersen, Henrik Nielsen - In ISMB’97 , 1997
"... Translation in eukaryotes does not always start at the first AUG in an mRNA, implying that context information also plays a role. This makes prediction of translation initiation sites a non-trivial task, especially when analysing EST and genome data where the entire mature mRNA sequence is not known ..."
Abstract - Cited by 76 (1 self) - Add to MetaCart
Translation in eukaryotes does not always start at the first AUG in an mRNA, implying that context information also plays a role. This makes prediction of translation initiation sites a non-trivial task, especially when analysing EST and genome data where the entire mature mRNA sequence is not known. In this paper, we employ artificial neural networks to predict which AUG triplet in an mRNA sequence is the start codon. The trained networks correctly classified 88 % of Arabidopsis and 85 % of vertebrate AUG triplets. We find that our trained neural networks use a combination of local start eodon context and global sequence information. Furthermore, analysis of false predictions shows that AUGs in frame with the actual start codon are more frequently selected than out-of-frame AUGs, suggesting that our networks use reading frame detection. A number of conflicts between neural network predictions and database annotations are analysed in detail, leading to identification of possible database errors.
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...the ribosome binds at the capped 5'-end of the mRNA and subsequently scans the sequence until the first start codon in a suitable context is found (Kozak 1983; 1984; Cigan & Donahue 1987; Joshi 1987; =-=Kozak 1989-=-). It has been reported that downstream AUGs are used as start codons in less than 10 % of investigated eukaryotic mRNAs (Kozak 1989; Yoon Phone: (+45) 45 25 24 84; Fax: (+45) 45 93 48 08, email: gorm...

Occludin: a novel integral membrane protein localizing at tight junctions

by Sachiko Tsukita, Shoichiro Tstlkita - 1777 – 1788 , 1993
"... Abstract. Recently, we found that ZO-1, a tight junction-associated protein, was concentrated in the so called isolated adherens junction fraction from the ..."
Abstract - Cited by 68 (1 self) - Add to MetaCart
Abstract. Recently, we found that ZO-1, a tight junction-associated protein, was concentrated in the so called isolated adherens junction fraction from the
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..., we considered that the ATG codon in position 21 is the initiation site for translation. This interpretation is confirmed by the existence of the consensus context for the initiation of translation (=-=Kozak, 1989-=-) at nucleotides 15-23. A search of the data bases identified no proteins with significant homology to occludin. In the deduced amino acid sequence of occludin, there appears to be no typical signal s...

Molecular characterization and tissue distribution of ZO-2, a tight junction protein homologous to ZO-1 and the Drosophila discs-large tumor suppressor protein

by Lylme A. Jesaitis, Daniel A. Goodenough - J. Cell , 1994
"... Abstract. ZO-1 is a 210-225-kD peripheral membrane protein associated with cytoplasmic surfaces of the zonula occludens or tight junction. A 160-kD polypeptide, designated ZO-2, was found to coimmunoprecipitate with ZO-1 from MDCK cell extracts prepared under conditions which preserve protein associ ..."
Abstract - Cited by 65 (3 self) - Add to MetaCart
Abstract. ZO-1 is a 210-225-kD peripheral membrane protein associated with cytoplasmic surfaces of the zonula occludens or tight junction. A 160-kD polypeptide, designated ZO-2, was found to coimmunoprecipitate with ZO-1 from MDCK cell extracts prepared under conditions which preserve protein associations

Synaptopodin: An Actin-associated Protein in Telencephalic Dendrites

by Renal Podocytes, Peter Mundel, Hans W. Heid, Thomas M. Mundel, Meike Krüger, Jochen Reiser, Wilhelm Kriz
"... Abstract. Synaptopodin is an actin-associated protein of differentiated podocytes that also occurs as part of the actin cytoskeleton of postsynaptic densities (PSD) and associated dendritic spines in a subpopulation of exclusively telencephalic synapses. Amino acid sequences determined in purified r ..."
Abstract - Cited by 60 (7 self) - Add to MetaCart
Abstract. Synaptopodin is an actin-associated protein of differentiated podocytes that also occurs as part of the actin cytoskeleton of postsynaptic densities (PSD) and associated dendritic spines in a subpopulation of exclusively telencephalic synapses. Amino acid sequences determined in purified rat kidney and forebrain synaptopodin and derived from human and mouse brain cDNA clones show no significant homology to any known protein. In particular, synaptopodin does not contain functional domains found in receptor-clustering PSD proteins. The open reading frame of synaptopodin encodes a polypeptide with a calculated M r of 73.7 kD (human)/74.0 kD (mouse) and an isoelectric point of 9.38 (human)/9.27 (mouse). Synaptopodin contains a high amount of proline (�20%) equally distributed
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...able from EMBL/GenBank/DDBJ under accession number H49442), sp47 (accession number R88417), and sp91 (accession number R90893) orientated from 5� to 3�, with clone sp17 containing a “Kozak sequence” (=-=Kozak, 1989-=-) before the start codon and clone sp91 ending with a polyA-tail (from a human brain cDNA library that covered the open reading frame [ORF] of human synaptopodin, except for a gap of 250 bases between...

The human immunodeficiency virus type 1 gag gene encodes an internal ribosome entry site

by Christopher B. Buck, Xuefei Shen, Michael A. Egan, Theodore C. Pierson, Christopher M. Walker, Robert F, Christopher B. Buck, Xuefei Shen, Michael A. Egan, Theodore C. Pierson, Christopher M. Walker, Robert F. Siliciano - J , 2001
"... Updated information and services can be found at: ..."
Abstract - Cited by 48 (1 self) - Add to MetaCart
Updated information and services can be found at:
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...ds to the 5� end of a capped mRNA (80, 81), commences scanning toward the 3� end, and initiates translation upon encountering an AUG codon in suitable context (often referred to as a “Kozak” context) =-=(47, 49, 50)-=-. The 60S ribosomal subunit is then recruited, and translation of a single polypeptide begins. Translation of some HIV-1 mRNAs can depart from this basic model in several ways. Translation of the pol ...

Cdc42 regulates anchorage-independent growth and is necessary for Ras transformation. Mol Cell Biol 17: 3449–3458

by R G Qiu, A Abo, F Mccormick, M Symons, Mol Cell Biol, Rong-guo Qiu, Arie Abo, Frank Mccormick, Marc Symons , 1997
"... Cdc42 regulates anchorage-independent growth and is necessary for Ras transformation. ..."
Abstract - Cited by 47 (1 self) - Add to MetaCart
Cdc42 regulates anchorage-independent growth and is necessary for Ras transformation.
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...GACATC to GGCCTTAAGTCACGCCTC ATCTCCTGCCGC, a region which contains the GTPase binding domain (GBD) (50), was cloned into the XbaI and EcoRI sites of the pyDF30 vector, which provides a Kozak sequence =-=(22)-=- and start ATG to a FLAG epitope at the 5� end. The insert in the resulting plasmid was checked by DNA sequencing. Expression of the WASP-derived GBD (WASP-GBD) was tested in transient transfection an...

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