Conserved Translational Frameshift in dsDNA Bacteriophage Tail Assembly Genes  Jun Xu, Roger W. Hendrix, Robert L. Duda  Molecular Cell  Volume 16, Issue 1, Pages 11-21 (October 2004) DOI: 10.1016/j.molcel.2004.09.006

Figure 1 Programmed Translational Frameshift Regions among the Tail Genes of Phages λ, HK97, and Mu (A–C) Frameshifting in λ was described previously (Levin et al., 1993); HK97 and Mu are considered in this report. (A) A map of the λ genes V, G/GT, and H shows the nested relationship of proteins gpG and gpGT, the frameshift product. Gene V encodes the major tail protein, and gene H encodes the tail length tape measure protein. Gene T was defined genetically, but no independent polypeptide is made from the T open reading frame. The vertical arrow between the G and T ORFs indicates the frameshift site, and this region and its translation in the relevant reading frames is expanded underneath. Ribosomes enter the slippery sequence GGGAAAG in the G reading frame (upper line) and either continue on to the end of gene G, 6 codons downstream, or, 3.5% of the time, shift back one base on the mRNA into the T reading frame and continue to the end of T, 145 codons downstream. (B) A map of the comparable region of the HK97 genome. The arrangement is the same as for λ, except that an extra gene (gene 15) and its associated transcription promoter and terminator are inserted between “T” and “H.” (C) A map of the comparable region of the Mu genome. Two alternative shifted frames are shown in the “T” region, and the vertical arrow indicates the site where the ribosomes shift into the −2 frame (see below). Molecular Cell 2004 16, 11-21DOI: (10.1016/j.molcel.2004.09.006)

Figure 2 Number of Frameshift Candidates Found by FSFinder with and without a Coding Potential Model The “No model” open bars indicate the number of candidates found when overlapping reading frames (>60 aa for both ORFs) with a −1 slippery sequence correctly positioned is the only criterion. The “Coding Potential model” solid bars show the number of candidates found when the requirement for good coding potential is added to the criteria. No manually identified G/GT frameshift sites listed in Table 1 and Supplemental Table S1 were rejected by this criterion. Notes: 1In F-pyocin, two final candidates are both in the G/GT overlapping region. Two slippery sequences are present. 2In PV83, three of the final candidates are likely to be false because they appear to arise from sequence errors (two in the portal gene and one in the integrase gene). Molecular Cell 2004 16, 11-21DOI: (10.1016/j.molcel.2004.09.006)

Figure 3 Evidence for “G/GT” Frameshifting in Diverse Phages (A) The regions corresponding to the λ-G/GT region from phages L5, φC31, Mu, TM4, and HK97 were cloned into a T7 promoter vector that has a T7 tag epitope tag, so that the N terminus of gene “G” of each phage was fused to the T7 tag leader peptide in the vector. The tagged proteins were expressed in BL21(DE3) cells and visualized by Western blotting with a monoclonal antibody against the T7 tag. The label above each lane indicates from which phage the extract was derived. Each lane has a lower, heavy band corresponding to the product of gene “G” of each phage and a higher, thinner band corresponding to the frameshifted product. The bands of the unshifted and primary frameshift products are labeled. In the L5 lane, the extra prominent band right above the “G” band is produced from a UGA readthrough (see below). (B) The mobility of each band shown in (A) was plotted against the predicted molecular weight. The mobility of all bands, except for the TM4 “G” band, correlates well with the predicted molecular weight. (C) The “G/GT” region of HK022 was directly cloned into the pT7-5 vector and expressed in BL21(DE3) cells. Two bands indicated as “gpG” and “gpGT” were amino-terminally sequenced, and both have the same N-terminal sequences as predicted for the “gpG” protein (HK022 gp13, data not shown). Molecular Cell 2004 16, 11-21DOI: (10.1016/j.molcel.2004.09.006)

Figure 4 Termination Codon Readthrough at the Slippery Region of Phage L5 (A) A map of the construct used to test for UGA readthrough. Rectangles represent segments of sequence, and the positions of termination codons are indicated by asterisks. The L5 “T*” segment is in the −1 frame relative to the others and connected to the L5 “G” by the −1 slippery sequence at the position shown by the vertical arrow. Predicted protein products are shown below. (B) Western blots with the indicated antibodies against the products of expression of the construct shown in (A). Molecular Cell 2004 16, 11-21DOI: (10.1016/j.molcel.2004.09.006)

Figure 5 Using Mass Spectrometry to Determine the Frameshift Sites in HK97 and Mu (A) Mass spectrum of HK97 “gpGT.” The deconvoluted mass of 26,612 is only 1.1 mass units less than predicted for the expected frameshift site and within the error range of the spectrometer (1 unit/10 kd). (B) Average masses of all possible −1 frameshift products from the overlap region of the “G” and “T” ORFs. (C) Overlap region of the HK97 “G” and “T” frames showing the frameshift site. Because the second codon at the slippery site specifies Lys in both reading frames, the data cannot distinguish between the Lysyl-tRNALys entering the ribosome before (K→V) or after (E→K) the shift. (D) Mass spectrum of Mu “gpGT.” The deconvoluted mass is 22,224.7, only 0.24 units more than predicted for a R→E −2 frameshift. (E) Average masses of all possible Mu “gpGT” −2 frameshift products. Predicted masses of products of +1 frameshifts (not shown) are all more than 70 mass units lower than the measured mass. (F) Overlapping region of Mu “G” and Mu “T” frames showing the −2 frameshift site. Molecular Cell 2004 16, 11-21DOI: (10.1016/j.molcel.2004.09.006)

Figure 6 Conservation and Possible Mechanism for the −2 Frameshift in Phage Mu (A) Nucleotide sequence alignment of three Mu-related phages based on an alignment of their “gpG” proteins (not shown) reveals a 9 base pair conserved sequence at the −2 frameshift site. In all three phages (group 6 in Table 1 and Supplemental Table S1), the −2/+1 frame will fill most of the gap between the end of “G” to the beginning of “H,” as illustrated for Mu in Figure 1C. (B) Basepairing possibilities at the Mu −2 slippery sequence. The lower line shows the mRNA sequence at the slippery site, with tick marks indicating codon boundaries in the incoming (0) frame. Shown above the mRNA sequence are the anticodon sequences for the Gly (CCC) and Arg (3′-GCI) tRNAs presumed to be in the P and A sites of the ribosome at the time of the shift. Vertical lines indicate base pairs between tRNA and mRNA at the three relative positions. Molecular Cell 2004 16, 11-21DOI: (10.1016/j.molcel.2004.09.006)