Computational identification of putative programmed
translational  frameshift sites

Shah, Atul A.; Giddings, Michael C.; Parvaz, Jasmin B.; Gesteland, Raymond F.; Atkins, John F.; Ivanov, Ivaylo P.

doi:10.1093/bioinformatics/18.8.1046

Cited by 74 publications

(61 citation statements)

References 22 publications

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“…3A), the sequence CTTAGGC is a slippery sequence that can promote z40% frameshift efficiency (Belcourt and Farabaugh 1990;Shah et al 2002;Farabaugh et al 2006). On the 0-frame, CTT-AGG is translated as Leu-Arg.…”

Section: Ser1mentioning

confidence: 99%

“…In addition, it will be of value to test this strain under various stress conditions, including nutrient deprivation, response to reactive oxygen species, and chemicals, to observe other phenotypes related to ABP140. Another intriguing feature of ABP140/TRM140 is the presence of an internal frameshift site (Asakura et al 1998) at which the slippery sequence, CUUAGGC, can promote a 40% frameshift frequency (Belcourt and Farabaugh 1990;Shah et al 2002;Farabaugh et al 2006). This sequence was first identified as the +1 frameshift site of the TYB gene of the Ty1 retrotransposon (Kawakami et al 1993;Voytas and Boeke 1993).…”

Section: Ser1mentioning

confidence: 99%

See 1 more Smart Citation

Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae

Noma¹,

Yi²,

Katoh³

et al. 2011

RNA

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Transfer RNAs contain various modified nucleotides that are introduced enzymatically at the post-transcriptional level. In Saccharomyces cerevisiae, 3-methylcytidine (m 3 C) is found at position 32 of the tRNAs for Thr and Ser. We used a systematic reverse genetic approach combined with mass spectrometry (ribonucleome analysis), and identified the actin-binding protein ABP140 as the protein responsible for m 3 C formation in both tRNA Thr1 and tRNA Ser1 . ABP140 consists of an N-terminal actinbinding sequence and a C-terminal S-adenosylmethionine (Ado-Met) binding motif. Deletion of the actin-binding sequence in ABP140 did not affect m 3 C formation, indicating that subcellular localization of ABP140 to actin filaments is not involved in tRNA modification. m 3 C formation in tRNA Thr1 could be reconstituted using recombinant Abp140p in the presence of Ado-Met, whereas m 3 C did not form in tRNA Ser1 in vitro, indicating the absence of a factor(s) required for tRNA Ser1 m 3 C formation. Thus, ABP140 has been designated TRM140 according to the preferred nomenclature. In addition, we observed a specific reduction of m 3 C formation in HeLa cells by siRNA-mediated knock down of the human ortholog of TRM140.

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Section: Ser1mentioning

confidence: 99%

Section: Ser1mentioning

confidence: 99%

Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae

Noma¹,

Yi²,

Katoh³

et al. 2011

RNA

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show abstract

“…Consequently, one might expect shift-prone sequences to be selected against and therefore underrepresented in coding sequences, especially those of highly expressed genes. Conversely, when shiftprone sequences occur, analysis for their possible utilization in gene expression is merited (25,52). …”

mentioning

confidence: 99%

Expression Levels Influence Ribosomal Frameshifting at the Tandem Rare Arginine Codons AGG_AGG and AGA_AGA in Escherichia coli

et al. 2005

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The rare codons AGG and AGA comprise 2% and 4%, respectively, of the arginine codons of Escherichia coli K-12, and their cognate tRNAs are sparse. At tandem occurrences of either rare codon, the paucity of cognate aminoacyl tRNAs for the second codon of the pair facilitates peptidyl-tRNA shifting to the ؉1 frame. However, AGG_AGG and AGA_AGA are not underrepresented and occur 4 and 42 times, respectively, in E. coli genes. Searches for corresponding occurrences in other bacteria provide no strong support for the functional utilization of frameshifting at these sequences. All sequences tested in their native context showed 1.5 to 11% frameshifting when expressed from multicopy plasmids. A cassette with one of these sequences singly integrated into the chromosome in stringent cells gave 0.9% frameshifting in contrast to two-to four-times-higher values obtained from multicopy plasmids in stringent cells and eight-times-higher values in relaxed cells. Thus, ؉1 frameshifting efficiency at AGG_AGG and AGA_AGA is influenced by the mRNA expression level. These tandem rare codons do not occur in highly expressed mRNAs.

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“…Experimental results of testing FSFinder2 on ~190 genomic and partial DNA sequences showed that it predicted frameshift sites efficiently and with greater sensitivity and specificity than other programs, because it focused on the overlapping regions of ORFs and prioritized candidate signals (For -1 frameshifts, sensitivity was 0.88 and specificity 0.97; for +1 frameshifts, sensitivity was 0.91 and specificity 0.94) [6,[9][10][11]. FSFinder2 has been successfully used to find unknown frameshift sites in the Shewanella genome.…”

Section: Resultsmentioning

confidence: 99%

Web Service for Finding Ribosomal Frameshifts

Byun

Moon

Han

2006

Computational Science – ICCS 2006

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Abstract. Recent advances in biomedical research have generated a huge amount of data and software to deal with the data. Many biomedical systems use heterogeneous data structures and incompatible software components, so integration of software components into a system can be hindered by incompatibilities between the components of the system. This paper presents an XML web service and web application program for predicting ribosomal frameshifts from genomic sequences. Experimental results show that the web service of the program is useful for resolving many problems with incompatible software components as well as for predicting frameshifts of diverse types. The web service is available at http://wilab.inha.ac.kr/fsfinder2.

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Computational identification of putative programmed translational frameshift sites

Abstract: Complete results from the analysis of S. cerevisiae are available on http://www.gesteland.genetics.utah.edu/freqAnalysis

Cited by 74 publications

References 22 publications

Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae

Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae

Expression Levels Influence Ribosomal Frameshifting at the Tandem Rare Arginine Codons AGG_AGG and AGA_AGA in Escherichia coli

Web Service for Finding Ribosomal Frameshifts

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