Phage Hunters Spring 2016
My Annotations
| Status | Page | Date/Time | GO Term (Aspect) | Reference | Evidence | Notes | Links |
|---|
| unacceptable | BPPHS:E | 2016-04-19 04:46:58 CDT | GO:0039640 cytolysis by virus via suppression of host peptidoglycan biosynthetic process (P) | PMID:10760296 | ECO:0000316 genetic interaction evidence used in manual assertion | Fig 2D – E-mediated lysis occurs in wt host cells (circle), is delayed in cells overexpressing MraY (MraY expressed from medium copy plasmid, square), and doesn’t occur in cells overexpressing an MraY mutant (MraY mutant expressed from same medium copy plasmid, triangle).
Suggests that E causes host lysis by inhibiting MraY. MraY is an enzyme involved in PG biosynthesis.
| challenge |
| acceptable | BPPHS:E | 2016-04-21 13:58:13 CDT | GO:0039635 suppression by virus of host peptidoglycan biosynthetic process (P) | PMID:11078734 | ECO:0000314 direct assay evidence used in manual assertion | Fig 3 – E expression inhibits [3H]-DAP incorporation into the cell wall (black square = E expression, black circle = no E expression)
Suggests that E inhibits cell wall biosynthesis – DAP is an amino acid unique to the bacterial cell wall
Fig 4B – E expression inhibits [3H]-DAP incorporation into PG biosynthesis lipid intermediates (black bar = no E expression, grey bar = E expression)
Suggests that E inhibits PG biosynthesis specifically – PG biosynthesis consists of three stages: nucleotide intermediate synthesis, lipid intermediate synthesis, and addition of PG precursors from lipid intermediates to actual PG – lipid intermediate synthesis is inhibited by E expression
| challenge |
| acceptable | BPPHS:E | 2016-04-21 13:58:13 CDT | GO:0039640 cytolysis by virus via suppression of host peptidoglycan biosynthetic process (P) | PMID:11078734 | ECO:0000314 direct assay evidence used in manual assertion | E causes host lysis:
Fig 3 – E expression causes decrease in cell density indicative of host cell lysis (clear square = E expression, clear circle = no E expression)
E inhibits PG biosynthesis:
Fig 3 – E expression inhibits [3H]-DAP incorporation into the cell wall is significantly inhibited by expression of E (black square = E expression, black circle = no E expression)
Suggests that E inhibits cell wall biosynthesis – DAP is an amino acid unique to the bacterial cell wall
Fig 4B – E expression inhibits [3H]-DAP incorporation into PG biosynthesis lipid intermediates is significantly inhibited by expression of E (black bar = no E expression, grey bar = E expression)
Suggests that E inhibits PG biosynthesis specifically – PG biosynthesis consists of three stages: nucleotide intermediate synthesis, lipid intermediate synthesis, and addition of PG precursors from lipid intermediates to actual PG – lipid intermediate synthesis is inhibited by E expression
| challenge |
| acceptable | BPQBE:D0U1G3 | 2016-05-06 16:00:02 CDT | GO:0039635 suppression by virus of host peptidoglycan biosynthetic process (P) | PMID:11423662 | ECO:0000314 direct assay evidence used in manual assertion | Fig 2 – A2 expression inhibits [3H]-DAP incorporation into the cell wall, causes degradation of cell wall (black circle = A2 expression, clear circle = no A2 expression)
Suggests that A2 inhibits cell wall biosynthesis – DAP is an amino acid unique to the bacterial cell wall
Used this particular Uniprot ID because it's the oldest entry - there are several entries for phage Qb A2 originating from differing strains, but the exact strain was not mentioned in the paper and no one in the lab knows (paper came out of Dr. Young's lab)
| challenge |
| acceptable | BPQBE:D0U1G3 | 2016-05-06 16:00:02 CDT | GO:0039640 cytolysis by virus via suppression of host peptidoglycan biosynthetic process (P) | PMID:11423662 | ECO:0000314 direct assay evidence used in manual assertion | A2 causes host lysis:
Fig 2 – A2 expression causes decrease in cell density indicative of host cell lysis (black square = A2 expression, clear square = no E expression)
A2 inhibits PG biosynthesis:
Fig 2 – A2 expression inhibits [3H]-DAP incorporation into the cell wall, causes degradation of cell wall (black circle = A2 expression, clear circle = no A2 expression)
Suggests that A2 inhibits cell wall biosynthesis – DAP is an amino acid unique to the bacterial cell wall
Used this particular Uniprot ID because it's the oldest entry - there are several entries for phage Qb A2 originating from differing strains, but the exact strain was not mentioned in the paper and no one in the lab knows (paper came out of Dr. Young's lab)
| challenge |
acceptable:4
unacceptable:1
requires_changes:0
flagged:0
Annotations challenged by LornaMin
| Status | Author,Group | Page | GO Term (Aspect) | Reference | Evidence | Links | Page history |
|---|
0 annotations fixed by LornaMin
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