A novel method of multiple alignment of biopolymer sequences

Brodsky, Leonid; Drachev, Alexander L.; Leontovich, Andrey M.; Feranchuk, Sergey

doi:10.1016/0303-2647(93)90063-i

Cited by 29 publications

(10 citation statements)

References 12 publications

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“…We refer to this 18-base sequence in the ODC 5Ј-UTR as the IRES regulatory element (RE). To analyze the effects on secondary structure caused by these mutations in the RE, we compared the wild-type and PY-mutated ODC IRES structures using an RNA folding algo-rithm (38,39). Although minor structural differences were predicted, the pyrimidine tract mutations are not expected to result in a complete restructuring of the ODC IRES (Supplemental Fig.…”

Section: Resultsmentioning

confidence: 99%

The Myotonic Dystrophy Type 2 Protein ZNF9 Is Part of an ITAF Complex That Promotes Cap-independent Translation

Gerbasi¹,

Link

2007

Molecular & Cellular Proteomics

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The 5-untranslated region of the ornithine decarboxylase (ODC) mRNA contains an internal ribosomal entry site (IRES). Mutational analysis of the ODC IRES has led to the identification of sequences necessary for cap-independent translation of the ODC mRNA. To discover novel IRES trans-acting factors (ITAFs), we performed a proteomics screen for proteins that regulate ODC translation using the wild-type ODC mRNA and a mutant version with an inactive IRES. We identified two RNA-binding proteins that associate with the wild-type ODC IRES but not the mutant IRES. One of these RNA-binding proteins, PCBP2, is an established activator of viral and cellular IRESs. The second protein, ZNF9 (myotonic dystrophy type 2 protein), has not been shown previously to bind IRES-like elements. Using a series of biochemical assays, we validated the interaction of these proteins with ODC mRNA. Interestingly ZNF9 and PCBP2 biochemically associated with each other and appeared to function as part of a larger holo-ITAF ribonucleoprotein complex. Our functional studies showed that PCBP2 and ZNF9 stimulate translation of the ODC IRES. Importantly these results may provide insight into the normal role of ZNF9 and why ZNF9 mutations cause myotonic dystrophy. Molecular & Cellular Proteomics 6:1049 -1058, 2007.Most eukaryotic translation initiation involves the interaction of the 43 S preinitiation complex (comprised of the 40 S ribosomal subunit plus initiation factors, Met-tRNA i , and GTP) with the 7-methylguanosine cap complex at the 5Ј-end of the mRNA (1). During such cap-dependent translation initiation, the 43 S preinitiation complex is recruited to the 5Ј-cap structure and scans the 5Ј-untranslated region (UTR).

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Section: Resultsmentioning

confidence: 99%

The Myotonic Dystrophy Type 2 Protein ZNF9 Is Part of an ITAF Complex That Promotes Cap-independent Translation

Gerbasi¹,

Link

2007

Molecular & Cellular Proteomics

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“…DNA sequencing of genomic and cDNA clones was performed using a Sequenase Version 2.0 Kit (Amersham) according to the supplier's instructions. Sequences were analyzed using the GENEBEE program [16].…”

Section: Methodsmentioning

confidence: 99%

Vinculin gene is non‐essential in Drosophila melanogaster

et al. 1997

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Vinculin is thought to be an important cytoskeletal protein in the linkage between actin cytoskeleton and integrin transmembrane receptors. We identified Vinculin (Vine) gene in the X chromosome of D. melanogaster. Drosophila vinculin is highly homologous in its N-and C-terminal domains both to mammalian and nematode vinculins, and contains internal repeats and proline-rich region typical for vinculins. The X chromosome rearrangement In(lLR)pn2a was found to disrupt Vine so that the coding sequence is interrupted by the (AAGAG)" satellite DNA. Northern analysis revealed that the Vine transcript is completely absent in the In(lLR)pn2a homozygous flies. Surprisingly, these Vine flies are viable and fertile. This finding highlights plasticity and adaptive capacity of cellular cytoskeletal and anchorage system. © 1997 Federation of European Biochemical Societies.

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“…4). The distance matrices were calculated by the Dayhoff matrix and the phylogenetic tree was constructed by cluster and topological algorithms with GeneBee software (7).…”

Section: Hinfi and Hindiii Restriction Sites Located In The M-isr Andmentioning

confidence: 99%

Identification of Carnobacterium Species by Restriction Fragment Length Polymorphism of the 16S-23S rRNA Gene Intergenic Spacer Region and Species-Specific PCR

Rachman

Hristova

Valcheva

et al. 2004

Appl Environ Microbiol

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The genus Carnobacterium is currently divided into the following eight species: Carnobacterium piscicola, C. divergens, C. gallinarum, C. mobile, C. funditum, C. alterfunditum, C. inhibens, and C. viridans. An identification tool for the rapid differentiation of these eight Carnobacterium species was developed, based on the 16S-23S ribosomal DNA (rDNA) intergenic spacer region (ISR). PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of this 16S-23S rDNA ISR was performed in order to obtain restriction profiles for all of the species. Three PCR amplicons, which were designated small ISR (S-ISR), medium ISR (M-ISR), and large ISR (L-ISR), were obtained for all Carnobacterium species. The L-ISR sequence revealed the presence of two tRNA genes, tRNA Ala and tRNA Ile , which were separated by a spacer region that varied from 24 to 38 bp long. This region was variable among the species, allowing the design of species-specific primers. These primers were tested and proved to be species specific. The identification method based on the 16S-23S rDNA ISR, using PCR-RFLP and specific primers, is very suitable for the rapid low-cost identification and discrimination of all of the Carnobacterium species from other phylogenetically related lactic acid bacteria.

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A novel method of multiple alignment of biopolymer sequences

Cited by 29 publications

References 12 publications

The Myotonic Dystrophy Type 2 Protein ZNF9 Is Part of an ITAF Complex That Promotes Cap-independent Translation

The Myotonic Dystrophy Type 2 Protein ZNF9 Is Part of an ITAF Complex That Promotes Cap-independent Translation

Vinculin gene is non‐essential in Drosophila melanogaster

Identification of Carnobacterium Species by Restriction Fragment Length Polymorphism of the 16S-23S rRNA Gene Intergenic Spacer Region and Species-Specific PCR

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