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Cacao

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Colocalizes withGO:1990220GroEL-GroES complexPMID:22234860ECO:0007163 IMP: Inferred from Mutant PhenotypeCellular Component
Figure 6 illustrates the insertion/substitution vector system of the Bacteriophage T4 in its host, Escherichia coli. While the figure shows a plaque assay, that visualization results from an in-frame deletion of the 39.2 gene of T4, which is believed to modulate the host's (E. coli) GroEL/GroES chaperone machine, which aids in the correct folding of both host and bacteriophage proteins. The phage T4 39.2 mutant (no 39.2 gene function) produced little to no plaques while the wild-type phage T4 produced plaques (Figure 6A). This shows that very little to none of the phage T4 survived in the mutant that did not have the 39.2 gene product.
complete
This annotation made on page: BPT4:D9IE38
By: JKelleher (group Team Purple A 2019) on 2019-04-11 08:27:49 CDT.




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Entry TypeChallenging User,GroupTime/DateChallenge ReasonPoints/Assessment
ChallengeKAtanasoff,
Team Blue A 2019		2019-04-15 10:02:49 CDT

The figure you cite shows neither that the gene product of 39.2 colocalizes with the GroEL-GroES complex, nor that it is a cellular component. A more appropriate GO term would probably be something that emphasizes how the 39.2 gene product is essential for T4 bacteriophage growth in certain hosts.

2
ChallengeCXie,
Team Red B 2019		2019-04-15 09:39:29 CDT

I disagree with the wording of this note, particularly “little to no plaques,” because plaques are still seen for the T4 39.2 phage mutant on the E. coli groEL44 host. This note also fails to distinguish between the E. coli groEL44 strain and the E. coli control. There is no explanation for the significance of a groE mutation. I disagree with the ECO term because the mutation is an “in-frame-deletion,” not an insertion. The ECO term should be ECO:0001175 Deletion mutation phenotypic evidence used in manual assertion.

1
Public
Assessment		Ivanerill2019-04-21 16:32:21 CDT

great work!

Acceptable
✔ Protein
✔ Publication
✔ Qualifier
✔ Go term
✔ Evidence
✔ With/From
✔ Notes
✔ Unique/Original
Public
Assessment		DanielRenfro2019-04-21 16:22:25 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference ECO ID ECO term name with/from Aspect Extension Notes Status
GO:1903332 regulation of protein folding PMID:22234860 ECO:0001165 IMP: Inferred from Mutant Phenotype P Gp39.2, which is a bacteriophage T4 protein, is believed to modulate the host's (E. coli) GroEL/GroES chaperone machine, which aids in the correct folding of both host and bacteriophage proteins. Gp39.2 is thought to play a part in correctly folding the E. coli host protein UmuC, which is part of the DNA Polymerase V complex. The authors believe that the GroEL/GroES complex is required for the DNA PolV to work and proofread in the bacteria cell. This relationship between Gp39.2 and DNA PolV is illustrated in Figure 5 where an E. coli mutant (that was only a mutant for isolation purposes for plating) was plated with and without the plasmid containing Gp39.2. The bacterium were then exposed to UV irradiation and were grown with and without arabinose, which showed which mutant bacteria had Gp39.2 in them. The Gp39.2 mutant bacteria were much more frequently seen while plating as opposed to the non-Gp39.2 mutant bacteria. complete
CACAO 13727
on BPT4:D9IE38
Flagged
Public
Assessment		Ivanerill2019-04-21 16:20:28 CDT

what is being manually counted?

Requires Changes
✗ Evidence
Public
Assessment		DanielRenfro2019-04-21 16:09:58 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference ECO ID ECO term name with/from Aspect Extension Notes Status
GO:1903332 regulation of protein folding PMID:22234860 ECO:0007118 IMP: Inferred from Mutant Phenotype P Gp39.2, which is a bacteriophage T4 protein, is believed to modulate the host's (E. coli) GroEL/GroES chaperone machine, which aids in the correct folding of both host and bacteriophage proteins. Gp39.2 is thought to play a part in correctly folding the E. coli host protein UmuC, which is part of the DNA Polymerase V complex. The authors believe that the GroEL/GroES complex is required for the DNA PolV to work and proofread in the bacteria cell. This relationship between Gp39.2 and DNA PolV is illustrated in Figure 5 where an E. coli mutant (that was only a mutant for isolation purposes for plating) was plated with and without the plasmid containing Gp39.2. The bacterium were then exposed to UV irradiation and were grown with and without arabinose, which showed which mutant bacteria had Gp39.2 in them. The Gp39.2 mutant bacteria were much more frequently seen while plating as opposed to the non-Gp39.2 mutant bacteria. complete
CACAO 13727
on BPT4:D9IE38
Flagged
Public
Assessment		Ivanerill2019-04-21 15:59:55 CDT

getting there for ECO, but not quite. all the authors do is look at the frequency (i.e. count) of spontaneous mutants capable of growing a colony on rifamycin plates

Requires Changes
✗ Evidence
Public
Assessment		DanielRenfro2019-04-21 15:53:08 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference ECO ID ECO term name with/from Aspect Extension Notes Status
GO:1903332 regulation of protein folding PMID:22234860 ECO:0007185 IMP: Inferred from Mutant Phenotype P Gp39.2, which is a bacteriophage T4 protein, is believed to modulate the host's (E. coli) GroEL/GroES chaperone machine, which aids in the correct folding of both host and bacteriophage proteins. Gp39.2 is thought to play a part in correctly folding the E. coli host protein UmuC, which is part of the DNA Polymerase V complex. The authors believe that the GroEL/GroES complex is required for the DNA PolV to work and proofread in the bacteria cell. This relationship between Gp39.2 and DNA PolV is illustrated in Figure 5 where an E. coli mutant (that was only a mutant for isolation purposes for plating) was plated with and without the plasmid containing Gp39.2. The bacterium were then exposed to UV irradiation and were grown with and without arabinose, which showed which mutant bacteria had Gp39.2 in them. The Gp39.2 mutant bacteria were much more frequently seen while plating as opposed to the non-Gp39.2 mutant bacteria. complete
CACAO 13727
on BPT4:D9IE38
Flagged
Public
Assessment		Ivanerill2019-04-21 15:40:46 CDTNo notes given.Requires Changes
✔ Go term
✗ Evidence
Public
Assessment		DanielRenfro2019-04-21 15:39:24 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference ECO ID ECO term name with/from Aspect Extension Notes Status
GO:1903332 regulation of protein folding PMID:22234860 ECO:0006023 IMP: Inferred from Mutant Phenotype P Gp39.2, which is a bacteriophage T4 protein, is believed to modulate the host's (E. coli) GroEL/GroES chaperone machine, which aids in the correct folding of both host and bacteriophage proteins. Gp39.2 is thought to play a part in correctly folding the E. coli host protein UmuC, which is part of the DNA Polymerase V complex. The authors believe that the GroEL/GroES complex is required for the DNA PolV to work and proofread in the bacteria cell. This relationship between Gp39.2 and DNA PolV is illustrated in Figure 5 where an E. coli mutant (that was only a mutant for isolation purposes for plating) was plated with and without the plasmid containing Gp39.2. The bacterium were then exposed to UV irradiation and were grown with and without arabinose, which showed which mutant bacteria had Gp39.2 in them. The Gp39.2 mutant bacteria were much more frequently seen while plating as opposed to the non-Gp39.2 mutant bacteria. complete
CACAO 13727
on BPT4:D9IE38
Flagged
Public
Assessment		DanielRenfro2019-04-21 15:33:27 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference ECO ID ECO term name with/from Aspect Extension Notes Status
GO:1903332 regulation of protein folding PMID:22234860 ECO:0005667 IMP: Inferred from Mutant Phenotype P Gp39.2, which is a bacteriophage T4 protein, is believed to modulate the host's (E. coli) GroEL/GroES chaperone machine, which aids in the correct folding of both host and bacteriophage proteins. Gp39.2 is thought to play a part in correctly folding the E. coli host protein UmuC, which is part of the DNA Polymerase V complex. The authors believe that the GroEL/GroES complex is required for the DNA PolV to work and proofread in the bacteria cell. This relationship between Gp39.2 and DNA PolV is illustrated in Figure 5 where an E. coli mutant (that was only a mutant for isolation purposes for plating) was plated with and without the plasmid containing Gp39.2. The bacterium were then exposed to UV irradiation and were grown with and without arabinose, which showed which mutant bacteria had Gp39.2 in them. The Gp39.2 mutant bacteria were much more frequently seen while plating as opposed to the non-Gp39.2 mutant bacteria. complete
CACAO 13727
on BPT4:D9IE38
Flagged
Public
Assessment		DanielRenfro2019-04-21 15:31:27 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference ECO ID ECO term name with/from Aspect Extension Notes Status
GO:1903332 regulation of protein folding PMID:22234860 ECO:0005667 IMP: Inferred from Mutant Phenotype P other:UniProtKB - D9IE38 Gp39.2, which is a bacteriophage T4 protein, is believed to modulate the host's (E. coli) GroEL/GroES chaperone machine, which aids in the correct folding of both host and bacteriophage proteins. Gp39.2 is thought to play a part in correctly folding the E. coli host protein UmuC, which is part of the DNA Polymerase V complex. The authors believe that the GroEL/GroES complex is required for the DNA PolV to work and proofread in the bacteria cell. This relationship between Gp39.2 and DNA PolV is illustrated in Figure 5 where an E. coli mutant (that was only a mutant for isolation purposes for plating) was plated with and without the plasmid containing Gp39.2. The bacterium were then exposed to UV irradiation and were grown with and without arabinose, which showed which mutant bacteria had Gp39.2 in them. The Gp39.2 mutant bacteria were much more frequently seen while plating as opposed to the non-Gp39.2 mutant bacteria. complete
CACAO 13727
on BPT4:D9IE38
Flagged
Public
Assessment		Ivanerill2019-04-21 15:26:15 CDT

GO is incorrect. Read your own notes and figure out what kind of function is 39.2 likely to have "thought to play a part in correctly folding the E. coli host protein UmuC, which is part of the DNA"

Remove the extension unless it is necessary.

As for the evidence, this pretty much sums it up: The Gp39.2 mutant bacteria were much more frequently seen while plating as opposed to the non-Gp39.2 mutant bacteria.

Requires Changes
✔ Protein
✔ Publication
✔ Qualifier
✗ Go term
✗ Evidence
✔ With/From
✔ Notes
✔ Unique/Original
Public
Assessment		DanielRenfro2019-04-21 14:17:24 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference ECO ID ECO term name with/from Aspect Extension Notes Status
GO:1900262 regulation of DNA-directed DNA polymerase activity PMID:22234860 ECO:0005667 IMP: Inferred from Mutant Phenotype P other:UniProtKB - D9IE38 Gp39.2, which is a bacteriophage T4 protein, is believed to modulate the host's (E. coli) GroEL/GroES chaperone machine, which aids in the correct folding of both host and bacteriophage proteins. Gp39.2 is thought to play a part in correctly folding the E. coli host protein UmuC, which is part of the DNA Polymerase V complex. The authors believe that the GroEL/GroES complex is required for the DNA PolV to work and proofread in the bacteria cell. This relationship between Gp39.2 and DNA PolV is illustrated in Figure 5 where an E. coli mutant (that was only a mutant for isolation purposes for plating) was plated with and without the plasmid containing Gp39.2. The bacterium were then exposed to UV irradiation and were grown with and without arabinose, which showed which mutant bacteria had Gp39.2 in them. The Gp39.2 mutant bacteria were much more frequently seen while plating as opposed to the non-Gp39.2 mutant bacteria. complete
CACAO 13727
on BPT4:D9IE38
Flagged
Public
Assessment		Ivanerill2019-04-21 09:49:28 CDT

GO term does not correspond with notes or evidence in article

Requires Changes
✗ Go term
Public
Assessment		DanielRenfro2019-04-21 07:39:24 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference ECO ID ECO term name with/from Aspect Extension Notes Status
GO:0033892 deoxyribonuclease (pyrimidine dimer) activity PMID:22234860 ECO:0001175 IMP: Inferred from Mutant Phenotype F other:UniProtKB - D9IE38 Figure 6 illustrates the insertion/substitution vector system of the Bacteriophage T4 in its host, Escherichia coli. While the figure shows a plaque assay, that visualization results from an in-frame deletion of the 39.2 gene of T4, which is believed to modulate the host's (E. coli) GroEL/GroES chaperone machine, which aids in the correct folding of both host and bacteriophage proteins. complete
CACAO 13727
on BPT4:D9IE38
Flagged
Public
Assessment		Ivanerill2019-04-20 04:51:12 CDT

Don't focus on the qualifiers/extensions. Figure out first what you are annotating.

Requires Changes
✔ Go term
Public
Assessment		DanielRenfro2019-04-19 20:27:35 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference ECO ID ECO term name with/from Aspect Extension Notes Status
GO:0033892 GroEL-GroES complex PMID:22234860 ECO:0001175 IMP: Inferred from Mutant Phenotype C other:UniProtKB - D9IE38 Figure 6 illustrates the insertion/substitution vector system of the Bacteriophage T4 in its host, Escherichia coli. While the figure shows a plaque assay, that visualization results from an in-frame deletion of the 39.2 gene of T4, which is believed to modulate the host's (E. coli) GroEL/GroES chaperone machine, which aids in the correct folding of both host and bacteriophage proteins. complete
CACAO 13727
on BPT4:D9IE38
Flagged
Public
Assessment		Ivanerill2019-04-18 09:19:23 CDT

See http://wiki.geneontology.org/index.php/Colocalizes_with and http://geneontology.org/docs/go-annotations/ regarding the qualifier "colocalizes with". Read and address the challenges. The experiments certainly do not demonstrate localization of the protein. If there is something to annotate here, it is likely not in Figure 6.

Requires Changes
✔ Protein
✔ Publication
✗ Qualifier
✗ Go term
✗ Evidence
✔ With/From
✗ Notes
✔ Unique/Original


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