Tape Measure Protein (TMP)

1. Tape Measure Protein (TMP) Structural proteins - determinant of phage tail length - gene length determines length of tail Is used and uses proteins during tail assembly; therefore, critical during assembly process [1, 2]

2. Localization of TM4 tmp motif 3 within proteins of mycobacteriophages Katherine Figueroa

3. Motifs Determined Three motifs within set of 14 mycobacteriophages [4] Proteins that have motif 3 have peptidoglycan hydrolysing activity [1] Easing efficient infection and DNA injection

5. Goal of Experiment To simulate the three motifs of Pedulla et al. in BioBIKE and localize motif 3 in proteins of mycobacteriophages

6. Motif 1

7. Motif 2

8. Motif 3

9. - Gathered tmps in mycobacteriophages using protein categories in subsystems [5] • - made list sequences similar to the tmp of mycobacteriophage TM4 • - scanned list of sequences similar to TM4 tmp applying defined motifs 1, 2, and 3

10. Determined what a bad result and good result looked like • Proceeded to apply motif 3 to the proteins of mycobacteriophages • - tougher than I thought • - still defining function to search for motif 3 in the proteins of all mycobacteriophages - Instead created a subset consisting of 14 mycobacteriophages

11. Results

12. References [1] Piuri, Mariana and Hatfull, Graham F. 2006. A peptidoglycan hydrolase motif within the mycobacteriophage TM4 tape measure protein promotes efficient infection of stationary phase cells. Molecular Microbiology;62(6): 1569-1585. [2] Katsura, I., and Hendrix, R.W. (1984) Length determination in bacteriophage lambda tails. Cell 39:691-698. [3] Pedulla, M.L., Ford, M.E., Houtz, J.M., Karthikeyan, T., Wadsworth, C., Lewis, J.A., et al. (2003) Origins of highly mosaic mycobacteriophage genomes. Cell 113: 171-182. [4] Mycobacteriophage Database [5] Elhai, J., Arnaud, T., Massar, J.P., Myers, J. K., Travers, M., Casey, J., Slupesky, M., Shrager, J. (2009) BioBIKE: a web-based, programmable, integrated biological knowledge base. Nucleic Acids Research 37: p.w28-w32.

13. Tandem Repeats of Similar Cluster Phages • Found the amino acid sequence’s of the following phages: • B1 Sub cluster – Scoot, Abu, & Chah • B2 Sub Cluster - Ares • B3 Sub Cluster- Akoma • B4 Sub Cluster - Fredrick • A2 Sub Cluster - L5 & D29

14. Sub Cluster B1 Motif

15. Sub Cluster Block Motifs

16. Alligned all sub slusters to look for tandem repeats Clustal Omega was used to find any similar tandem repeats within Sub Clusters B1, B2, B3, B4, & A2

17. Phylogenic Relationship

18. Results • Unable to find any similar tandem repeats within sub clusters B1, B2, B3, B4, and A2 • Results indicate that within sub cluster B, many identical amino acids were found in the same position within the tmp • Sub Cluster A2 and B1-4 did show some similar over lapping amino acid sequences in similar positions within their tmps • Phylogenic tree shows that sub clusters A2 and B1-4 do share a common ancestry in their tmp

19. References The evolution of the tape measure protein: units, duplications and losses: Belcaid M, Bergeron A, Poisson G. BMC Bioinformatics. 2011 Oct 5;12 Suppl 9:S10. doi: 10.1186/1471-2105-12-S9-S10.http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3271669/ Length Determination in Bacteriophage Lambda Tails. Katsura, I and Hendrix, R. Cell, Vol . 39, 691-698, December 1984. http://ac.els-cdn.com/0092867484904768/1-s2.0-0092867484904768-main.pdf?_tid=46972fa4-9c69-11e2-b6bc-00000aab0f26&acdnat=1364998854_34031474c286eed57d3f1aadfd1a1d92 Mechanism of Length Determination in Bacteriophage Lambda Tail. Katsura, Isao. Department of Biology, College of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153, Japan. Adv. Biophys., Vol. 26, pp. 1-18 (1990).