Superinfection Exculsion and Restriction Resistance

of Mycobacteriophages

Superinfection Exclusion Proteins in Mycobacteriophages

Keith Herbert

What is Superinfection Exclusion?

What I Wanted to Know

• Do mycobacteriophages have superinfection exclusion genes?

• If so, which phages?• If so, what kind of

superinfection exclusion?

What I Did

MrGordo 1 MSNIWDQPAY QPGYYPKADA AARAAKRKGR IEGWLALGAI VALIVLMS-I KBG 1 MSNIWDQPAY QPGYYPQADA AARAAKRKGR IEGWLALGAI VALIVLMS-I SkiPole 1 MSNIWDQPAY QPGYYPQADA AARAAKRKGR IEGWLALGAI VALIVLMS-I Lesedi 1 MSNIWDQPAY QPGYYPQADA AARAAKRKGR IEGWLALGAI VALIVLMS-I DD5 1 MSNIWDQPAY QPGYYPQADA AARAAKRKGR IEGWLALGAI VALIVLMS-I Lockley 1 MSNIWDQPAY QPGYYPQADA AARAAKRKGR IEGWLALGAI VALIVLMS-I BAKA 1 MSNIWDQPAY QPGYYPQADA AARAAKRKGR IEGWLALGAI VALIVLMS-I JC27 1 MSNIWDQPAY QPGYYPQADA AARAAKRKGR IEGWLALGAI VALIVLMS-I Museum 1 MSNIWDQPAY QPGYYPQADA AARAAKRKGR IEGWLALGAI VALIVLMS-I BPBiebs31 1 MSNIWDQPAY QPGYYPQADA AARAAKRKGR IEGWLALGAI VALIVLMS-I Pari 1 MSNIWDQPAY QPGYYPQADA AARAAKRKGR IEGWLALGAI VALIVLMS-I Bethlehem 1 MSNIWDQPAY QPGYYPQADA AARAAKRKGR IEGWLALGAI VALIVLMS-I Solon 1 MSNIWDQPAY QPGYYPQADA AARAAKRKGR IEGWLALGAI VALIVLMS-I Kugel 1 MSNIWDQPAY QPGYYPQADS AARAAKRKGR IEGWLALGAI VALIVLMS-I KSSJEB 1 MSNIWDQPAY QPGYYPQADA AARAAKRKGR IEGWLALGAI VALIVLMS-I Jasper 1 MSNIWDQPAY QPGYYPQADA AARAAKRKGR IEGWLALGAI VALIVLMS-I Doom 1 MSNIWDQPAY QPAY---APT SKWNARRLAG LG-ILAV-LL VAMIAMEPRV Myc-U2 1 MSNIWDQPAY WASQP--APV RKWNARRLAG LG-ILAV-LL VAMIAMEPRV vB_EcoM-VR7 1 ---------- ---------- ---------- ------METI IAGTFVLG-- IME08 1 ---------- ---------- ---------- ------MEAL IVSAGVLG-- MrGordo 50 SPGHALLVVL GSAYFAPTIV AYYRKASLKQ PVAVINVFLG WTFIGWVVAL KBG 50 SPGHALLVVL GSAYFAPTIV AYYRKASLKQ PVAVINVFLG WTFIGWVVAL SkiPole 50 SAGHALLVVL GTAYFVPTIV AYYRKASLKQ PVAVINVFLG WTFIGWVVTL Lesedi 50 SPGHALLVVL GAAYFVPTIV AYYRKASLKQ PVAVINVFLG WTFIGWVVAL DD5 50 SPSHALLVVF GTAYFVPTIV AYYRKASLKQ PVAVINVFLG WTFIGWVVAL Lockley 50 SPSHALLVVF GTAYFVPTIV AYYRKASLKQ PVAVINVFLG WTFIGWVVAL BAKA 50 SPGHALLVVF GTAYFVPTIV AYYRKASLKQ PVAVINVFLG WTFIGWVVAL JC27 50 SPSHALLVVF GTAYFVPTIV AYYRKASLKQ PVAVINVFLG WTFVGWVVAL Museum 50 SPSHALLVVF GTAYFVPTIV AYYRKASLKQ PVAVINVFLG WTFVGWVVAL BPBiebs31 50 SPSHALLVVL GTAYFVPTIV AYYRKASLKQ PVAVINVFLG WTFVGWVVAL Pari 50 SPSHALLVVL GTAYFVPTIV AYYRKASLKQ PVAVINVFLG WTFIGWVVAL Bethlehem 50 SPSHALLVVL GTAYFVPTIV AYYRKASLKQ PVAVINVFLG WTFIGWVVAL Solon 50 SPSHALLVVL GTAYFVPTIV AYYRKASLKQ PVAVINVFLG WTFIGWVVAL Kugel 50 SPSHALLVVL GTAYFVPTIV AYYRKASLKQ PVAVINVFLG WTFIGWVVAL KSSJEB 50 SPSHALLVVL GAAYFVPTIV AYYRKASLKQ PVAVINVFLG WTFIGWVVAL Jasper 50 SPSHALLVVF GAAYFVPTIV AYYRKASLKQ PVAVINVFLG WTFIGWVVAL Doom 46 FGPIAFTGLF IGVYLLPTLV ATVRKSHLLG PVTVVNLLLG WTFIGWVVAL Myc-U2 47 FGPIAFTGLF IGVYLLPTLV ATVRKSHLQG PVTVVNLFLG WTFIGWVVAL vB_EcoM-VR7 13 AGSLFLAALA ---YFLPWII ALLRGTRSNV GIFFINLLFG WTMIGWVIAL IME08 13 FGSLAIMFIG ---YFLPWIL ALLRGTRSNV GIFFLNLLLG WTMIGWVVAL KBG 100 AMAVK----- ---------- - SkiPole 100 AMAVKN---- ---------- - Lesedi 100 AMAVK----- ---------- - DD5 100 AMAMGKKQ-- ---------- - Lockley 100 AMAMGKKQ-- ---------- - BAKA 100 AMAVK----- ---------- - JC27 100 AMAVKDSRG- ---------- - Museum 100 AMAVKR---- ---------- - BPBiebs31 100 AMAVKK---- ---------- - Pari 100 AMAVKK---- ---------- - Bethlehem 100 AMAVKK---- ---------- - Solon 100 AMAVKDSRG- ---------- - Kugel 100 AMAVKDSRG- ---------- - KSSJEB 100 AMAVKDSRG- ---------- - Jasper 100 AMAVKDSRG- ---------- - Doom 96 AMAVKDSRG- ---------- - Myc-U2 97 AMAVKK---- ---------- - vB_EcoM-VR7 60 IWALVAERKS NAQVIIIKET K IME08 60 IWAIVAERKS NAQIIIVKQ- - consensus 101 *:

QUERY Q-START Q-END TARGET T-START T-END E-VALUE %ID 1. vB_EcoM-VR7.p-VR7_gp051 12 63 Lesedi.p-Lesedi-0066 52 103 4.0d-6 40.38 2. vB_EcoM-VR7.p-VR7_gp051 16 67 Solon.p-SOLON_69 56 107 5.0d-6 40.38 3. vB_EcoM-VR7.p-VR7_gp051 16 67 Kugel.p-Kugel-0070 56 107 5.0d-6 40.38 4. vB_EcoM-VR7.p-VR7_gp051 12 63 BAKA.p-BAKA-0184 52 103 5.0d-6 40.38 5. vB_EcoM-VR7.p-VR7_gp051 16 67 KSSJEB.p-KSSJEB-0065 56 107 5.0d-6 40.38 6. vB_EcoM-VR7.p-VR7_gp051 16 67 Jasper.p-Jasper_72 56 107 6.0d-6 40.38 7. vB_EcoM-VR7.p-VR7_gp051 16 63 DD5.p-DD5_71 56 103 6.0d-6 41.67 8. vB_EcoM-VR7.p-VR7_gp051 16 63 Pari.p-Pari-0072 56 103 6.0d-6 41.67 9. vB_EcoM-VR7.p-VR7_gp051 16 63 Bxb1.p-Bxb1-1064 56 103 6.0d-6 41.67 10. vB_EcoM-VR7.p-VR7_gp051 16 63 Bethlehem.p-Bethlehem_gp75 56 103 6.0d-6 41.67 11. vB_EcoM-VR7.p-VR7_gp051 16 63 Lockley.p-Lockley_70 56 103 6.0d-6 41.67 12. vB_EcoM-VR7.p-VR7_gp051 16 63 BPBiebs31.p-BPBiebs31-0072 56 103 8.0d-6 39.58 13. vB_EcoM-VR7.p-VR7_gp051 11 63 SkiPole.p-SkiPole-0080 49 103 8.0d-6 40.0 14. vB_EcoM-VR7.p-VR7_gp051 12 63 MrGordo.p-MrGordo-0069 52 103 8.0d-6 40.38 15. vB_EcoM-VR7.p-VR7_gp051 16 67 JC27.p-JC27-0070 56 107 8.0d-6 38.46 16. vB_EcoM-VR7.p-VR7_gp051 12 63 KBG.p-KBG_70 52 103 8.0d-6 40.38 17. vB_EcoM-VR7.p-VR7_gp051 16 63 Museum.p-Museum-0068 56 103 1.0d-5 39.58 18. vB_EcoM-VR7.p-VR7_gp051 23 67 Doom.p-Doom-0063 59 103 2.0d-5 42.22 19. vB_EcoM-VR7.p-VR7_gp051 23 63 Myc-U2.p-U2_gp66 60 100 3.0d-5 41.46

What I Found

• Group of phages with nearly identical protein

closely matching two SIE proteins of

enterobacteriophages

• Surprising. Expected other gram positive phages due

to cell wall differences

• Compared these to list of SIE proteins known

from in vitro experiments.

• Close match with Imm protein of Coliphage

T4

The case of the missing palindromes

Tayab Waseem

phages can defend themselves against host restriction enzymes by ridding themselves of recognition sites

Phage defense

Expected Values of 64 palindromes

Observed Values of 64 palindromes

Use chi-squared test

Total number of observed zero’s

Sequence recognized by a restriction enzyme from the Enterobacteriaceae

GGATCC -61% AAGCTT- 53% CCTAGG- 60 %

Sequence recognized by a restriction enzyme from a Bacillus species as well as Enterobacteriaceae.

GAGCTC- 52% CGGCCG- 64% GGGCCC- 75%

Much more accurate results if I use the chi-squared test and then compare.

Further experimentation