Standard Operating Procedure (SOP) for detecting Ribosomal
Slippages
Natalia Mikhailova, Genome Biology Program, JGI
SOP for detecting ribosomal slippage for “peptide chain release factor 2”
1. Check if the gene annotated as “peptide chain release factor 2”, is shorter then
some of the homologs. If it is, then very likely there is a ribosomal slippage in that
gene.
2. Find the start sequence by performing blastx of the nucleotide sequence
upstream of the gene.
3. To locate the exact place of the slippage try to find the nucleotide sequence
Ctttgac
The ribosomal slippage would be ctt-t-gac (it also could be ctt-t-aac)
Ctt would be on the one frame, and gac – on the different frame.
4. Merge frames and determine a new start codon by the alignment of the
homologous genes.
5. Annotate an extended gene in Artemis file as
/exception="ribosomal slippage"
References
1. Craigen,W.J., Cook,R.G., Tate,W.P. and Caskey,C.T.
Bacterial peptide chain release factors: conserved primary structure and possible frameshift
regulation of release factor 2
Proc. Natl. Acad. Sci. U.S.A. 82 (11), 3616-3620 (1985)
2. Lee,C.C., Kohara,Y., Akiyama,K., Smith,C.L., Craigen,W.J. and Caskey,C.T.
Rapid and precise mapping of the Escherichia coli release factor genes by two physical
approaches
J. Bacteriol. 170 (10), 4537-4541 (1988)
3. Yanga Byuna, Sanghoon Moona and Kyungsook Han
A general computational model for predicting ribosomal frameshifts in genome
sequences
Computers in Biology and Medicine
Volume 37, Issue 12, December 2007, Pages 1796-1801
4. Michael Chandler and Olivier Fayet
Translational frameshifting in the control of transposition in bacteria
Molecular Microbiology
Volume 7 Issue 4 Page 497-503, February 1993
SOP for detecting ribosomal slippages in transposases:
1. If a gene reported as “short” is annotated as a transposase, then check if the
upstream gene is annotated also as a transposase.
2. If upstream gene is annotated also as a transposase, then blastx the
nucleotide sequence of the region beginning at the start of the upstream gene
and ending at the end of the short gene.
3. If the blastx gives long versions of the transposase, locate the place of the
frameshift by looking at the pair-wise amino acid alignment.
4. Check if that place has a potential for a ribosomal slippage. That place should
contain a heptanucleotide slippery sequence XXXYYYN (where X=A,G or T and
Y=A or T)
5. If the location of the frameshift has a potential for a ribosomal slippage, then
merge the genes and annotate the resulting gene as having a frameshift:
/exception="ribosomal slippage"
References
1. Yanga Byuna, Sanghoon Moona and Kyungsook Han
A general computational model for predicting ribosomal frameshifts in genome
sequences
Computers in Biology and Medicine
Volume 37, Issue 12, December 2007, Pages 1796-1801
2. Sanghoon Moon, Yanga Byun, Hong-Jin Kim, Sunjoo Jeong, and Kyungsook Han
Predicting genes expressed via −1 and +1 frameshifts
Nucleic Acids Res. 2004; 32(16): 4884–4892.
Published online 2004 September 15. doi: 10.1093/nar/gkh829
3. Olga L. Gurvich, Pavel V. Baranov, Jiadong Zhou, Andrew W. Hammer,
Raymond F. Gesteland and John F. Atkins
Sequences that direct significant levels of frameshifting are frequent in coding
regions of Escherichia coli
The EMBO Journal (2003) 22, 5941–5950
doi:10.1093/emboj/cdg561
4. Nina Mejlhede, John F. Atkins, and Jan Neuhard
Ribosomal −1 Frameshifting during Decoding of Bacillus subtilis cdd Occurs at
the Sequence CGA AAG
Bacteriol. 1999 May; 181(9): 2930–2937
5. Michael Chandler and Olivier Fayet
Translational frameshifting in the control of transposition in bacteria
Molecular Microbiology
Volume 7 Issue 4 Page 497-503, February 1993
A-AAA-AAG (From publication 5.)
Examples of frameshift sequences
CCCCCCTTTTT
Transposase
AAAAAAGGGGGG
GGGGGAAAAAAA
GGGGGAAACAAA
TTTTTCCCCC (AAAAAGGGGG)
TTGTTCCCCC (AACAAGGGGG)
AAAAAGGGGG