Tape Measure Protein (TMP)

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 TM4 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

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

Goal of Experiment

Motif 1

Motif 2

Motif 3

- made list sequences similar to the tmp of mycobacteriophage TM4

- Gathered tmps in mycobacteriophages using protein categories in subsystems [5]

- scanned list of sequences similar to TM4 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 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.

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

Sub Cluster B1 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 B1, B2, B3, B4, & A2

Phylogenic Relationship

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

References1.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/

2.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

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).