Tape Measure Protein TMP Structural proteins determinant of

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]

Localization of TM 4 tmp motif 3 within proteins of mycobacteriophages Katherine Figueroa

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

Goal of Experiment To simulate three motifs of Pedulla et al. in Bio. BIKE and localize motif 3 in proteins of mycobacteriophages

Motif 1

Motif 2

Motif 3

- Gathered tmps in mycobacteriophages using protein categories in subsystems [5] - made list sequences similar to the tmp of mycobacteriophage TM 4 - scanned list of sequences similar to TM 4 tmp applying defined motifs 1, 2, and 3

- 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

Results

References [1] Piuri, Mariana and Hatfull, Graham F. 2006. A peptidoglycan hydrolase motif within the mycobacteriophage TM 4 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) Bio. BIKE: a web-based, programmable, integrated biological knowledge base. Nucleic Acids Research 37: p. w 28 -w 32.

Tandem Repeats of Similar Cluster Phages • • • Found the amino acid sequence’s of the following phages: B 1 Sub cluster – Scoot, Abu, & Chah B 2 Sub Cluster - Ares B 3 Sub Cluster - Akoma B 4 Sub Cluster - Fredrick A 2 Sub Cluster - L 5 & D 29

Sub Cluster B 1 Motif

Sub Cluster Block Motifs

Alligned all sub slusters to look for tandem repeats Clustal Omega was used to find any similar tandem repeats within Sub Clusters B 1, B 2, B 3, B 4, & A 2

Phylogenic Relationship

Results • Unable to find any similar tandem repeats within sub clusters B 1, B 2, B 3, B 4, and A 2 • Results indicate that within sub cluster B, many identical amino acids were found in the same position within the tmp • Sub Cluster A 2 and B 1 -4 did show some similar over lapping amino acid sequences in similar positions within their tmps • Phylogenic tree shows that sub clusters A 2 and B 1 -4 do share a common ancestry in their tmp

References 1. 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: S 10. doi: 10. 1186/1471 -2105 -12 -S 9 S 10. http: //www. ncbi. nlm. nih. gov/pmc/articles/PMC 3271669/ 2. Length Determination in Bacteriophage Lambda Tails. Katsura, I and Hendrix, R. Cell, Vol. 39, 691 -698, December 1984. http: //ac. elscdn. com/0092867484904768/1 -s 2. 0 -0092867484904768 main. pdf? _tid=46972 fa 4 -9 c 69 -11 e 2 -b 6 bc 00000 aab 0 f 26&acdnat=1364998854_34031474 c 286 eed 57 d 3 f 1 aadfd 1 a 1 d 92 3. 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).