Tape Measure Protein (TMP)
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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]
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Localization of TM4 tmp motif 3 within proteins of mycobacteriophages
Katherine Figueroa
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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
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To simulate the three motifs of Pedulla et al. in BioBIKE and localize motif 3 in proteins of mycobacteriophages
Goal of Experiment
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Motif 1
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Motif 2
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Motif 3
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- 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
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- 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
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Results
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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.
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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
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Sub Cluster B1 Motif
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Sub Cluster Block Motifs
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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
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Phylogenic Relationship
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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
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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).