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Cacao

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Contributes toGO:0098009viral terminase, large subunitPMID:11866517ECO:0000314 IDA: Inferred from Direct AssayCellular Component
This article is discussing a protein that bundles DNA (terminase) and the role of it's large subunit in moving DNA to it's final destination. Other experiments had already established that terminase is involved in physically cutting DNA and other early packaging processes. But in previous studies, the mechanism of how exactly DNA ends up inside of the phage's head had not been explored. The researchers in this experiment wanted to show that the large subunit of terminase helps move DNA into the phage's head (this was the researcher's assertion). The lambda bacteriophage was used in this experiment, and mutant A genes (from this phage's terminase large subunit) were studied. The rationale and purpose of the experiment is found in the abstract.


Table 5 is a good summary of this experiment and provides evidence that supports the researchers' assertion. Various phages with different types of defected A genes were observed in vivo to see how much DNA was packaged inside the phage's head. The amount varied according to the specific mutant and is recorded on the table as a percentage. This provides evidence for the researchers' hypothesis: that the A genes (which are part of the phage's terminase large subunit) actually do help package DNA into the phage's head, which provides evidence for the researchers' hypothesis.


Article citation: Duffy, Carol, and Michael Feiss. "The large subunit of bacteriophage λ’s terminase plays a role in DNA translocation and packaging termination." Journal of molecular biology 316.3 (2002): 547-561.

complete
This annotation made on page: LAMBD:TERL
By: TNaqvi (group Team Blue B 2019) on 2019-03-11 13:57:35 CDT.



TeamPoints
Team Blue B 20195




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Entry TypeChallenging User,GroupTime/DateChallenge ReasonPoints/Assessment
Public
Assessment		Ivanerill2019-04-21 04:29:43 CDTNo notes given.Acceptable
✔ Protein
✔ Publication
✔ Qualifier
✔ Go term
✔ Evidence
✔ With/From
✔ Notes
✔ Unique/Original
Public
Assessment		DanielRenfro2019-04-20 15:12:04 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:0019073 viral DNA genome packaging PMID:11866517 ECO:0007101 IMP: Inferred from Mutant Phenotype P Researchers wanted to show that gpA (found in the terminase large subunit) helps package phage DNA. A lambda bacteriophage was used in this experiment and various gpA mutants were cut (with a restriction endonuclease) and cloned into this phage; the amount of DNA packaged was determined experimentally by quantifying it in vivo. Table 5 shows how a normal lambda-P1 Sam7 phage with no mutated gpA was able to package 100% of its DNA. But when the same phage contained any type of mutated gpA, the percentage of DNA packaged decreased dramatically. complete
CACAO 13561
on LAMBD:TERL
Flagged
Public
Assessment		Ivanerill2019-04-20 04:45:17 CDT

This is what the authors say about their method: "DNA packaging activity was quantified using the above protocol for the puri®cation of packaged DNA. The undigested DNAs were electrophoresed through a 0.8 % agarose gel containing 0.5 mg/ml ethidium bromide. After electrophoresis the DNA was transferred to a GeneScreen Plus membrane (NENTM Life Science Products Inc., Boston, MA). DNA hybridizations were performed using 32P-labeled l DNA as a probe. An InstantImagerTM (Packard, Meriden, CT) electronic autoradiographer was used to quantify the hybridized, radiolabeled probe."

Look at the children for the term you suggest (ECO:0005519), see if you can find something that matches.

Requires Changes
✔ Protein
✔ Publication
✔ Qualifier
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Public
Assessment		DanielRenfro2019-04-18 18:36:31 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:0019073 viral DNA genome packaging PMID:11866517 ECO:0007737 IMP: Inferred from Mutant Phenotype P Researchers wanted to show that gpA (found in the terminase large subunit) helps package phage DNA. A lambda bacteriophage was used in this experiment and various gpA mutants were cut (with a restriction endonuclease) and cloned into this phage; the amount of DNA packaged was determined experimentally by quantifying it in vivo. Table 5 shows how a normal lambda-P1 Sam7 phage with no mutated gpA was able to package 100% of its DNA. But when the same phage contained any type of mutated gpA, the percentage of DNA packaged decreased dramatically. complete
CACAO 13561
on LAMBD:TERL
Flagged
Public
Assessment		Ivanerill2019-04-18 10:51:29 CDT

Noted before: it's "gene A" or "gpA", not "A genes". The ECO term can be further specified, in that DNA is measured; look for it.

Requires Changes
✔ Protein
✔ Publication
✔ Qualifier
✔ Go term
✗ Evidence
✔ With/From
✗ Notes
✔ Unique/Original
Public
Assessment		DanielRenfro2019-04-17 10:42:06 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:0019073 viral DNA genome packaging PMID:11866517 ECO:0007685 IMP: Inferred from Mutant Phenotype P Researchers wanted to show that the terminase large subunit’s A genes help package phage DNA. A lambda bacteriophage was used in this experiment and various mutant A genes were cut (with a restriction endonuclease) and cloned into this phage; the amount of DNA packaged was determined experimentally in vivo. Table 5 shows how a normal lambda-P1 Sam7 phage with no mutated A genes was able to package 100% of its DNA. But when the same phage contained any type of mutated A gene, the percentage of DNA packaged decreased dramatically. complete
CACAO 13561
on LAMBD:TERL
Flagged
Public
Assessment		DanielRenfro2019-04-17 10:41:29 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:0019073 viral DNA genome packaging PMID:11866517 ECO:0007685 IMP: Inferred from Mutant Phenotype P Researchers wanted to show that the terminase large subunit’s A genes help package phage DNA. A lambda bacteriophage was used in this experiment and various mutant A genes were cut (with a restriction endonuclease) and cloned into this phage; the amount of DNA packaged was determined experimentally in vivo. Table 5 shows how a normal lambda-P1 Sam7 phage with no mutated A genes was able to package 100% of its DNA. But when the same phage contained any type of mutated A gene, the percentage of DNA packaged decreased dramatically. complete
CACAO 13561
on LAMBD:TERL
Flagged
Public
Assessment		Ivanerill2019-04-08 17:39:59 CDT

Table 5 does not show localization, much less to the terminase subunit. The ECO term can be further specified, in that DNA is measured. Please reword to "gene A" or gpA across. Notes should be rewritten accordingly. Right now they point to a different GO term.

Requires Changes
✔ Protein
✔ Publication
✔ Qualifier
✗ Go term
✗ Evidence
✔ With/From
✗ Notes
✔ Unique/Original
Public
Assessment		DanielRenfro2019-04-07 14:53:58 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:0019073 viral DNA genome packaging PMID:11866517 ECO:0007119 IMP: Inferred from Mutant Phenotype P Researchers wanted to show that the terminase large subunit’s A genes help package phage DNA. A lambda bacteriophage was used in this experiment and various mutant A genes were cut (with a restriction endonuclease) and cloned into this phage; the amount of DNA packaged was determined experimentally in vivo. Table 5 shows how a normal lambda-P1 Sam7 phage with no mutated A genes was able to package 100% of its DNA. But when the same phage contained any type of mutated A gene, the percentage of DNA packaged decreased dramatically. complete
CACAO 13561
on LAMBD:TERL
Flagged
Public
Assessment		DanielRenfro2019-04-07 13:49:22 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:0019073 viral DNA genome packaging PMID:11866517 ECO:0007119 IMP: Inferred from Mutant Phenotype P Researchers wanted to show that the terminase large subunit’s A genes help package phage DNA; a lambda bacteriophage was used in this experiment and various mutant A genes were cut (with a restriction endonuclease) and cloned into this phage. Table 5 shows how a normal lambda-P1 Sam7 phage with no mutated A genes was able to package 100% of its DNA. But when the same phage contained any type of mutated A gene, the percentage of DNA packaged decreased dramatically. complete
CACAO 13561
on LAMBD:TERL
Flagged
Public
Assessment		DanielRenfro2019-04-07 12:28:05 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:0019073 viral terminase, large subunit PMID:11866517 ECO:0007119 IGC: Inferred from Genomic Context C Researchers wanted to show that the terminase large subunit’s A genes help package phage DNA; a lambda bacteriophage was used in this experiment and various mutant A genes were cut (with a restriction endonuclease) and cloned into this phage. Table 5 shows how a normal lambda-P1 Sam7 phage with no mutated A genes was able to package 100% of its DNA. But when the same phage contained any type of mutated A gene, the percentage of DNA packaged decreased dramatically. complete
CACAO 13561
on LAMBD:TERL
Flagged
Public
Assessment		DanielRenfro2019-04-07 12:27:34 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:0019073 viral terminase, large subunit PMID:11866517 ECO:0007119 IGC: Inferred from Genomic Context C Researchers wanted to show that the terminase large subunit’s A genes help package phage DNA; a lambda bacteriophage was used in this experiment and various mutant A genes were cut (with a restriction endonuclease) and cloned into this phage. Table 5 shows how a normal lambda-P1 Sam7 phage with no mutated A genes was able to package 100% of its DNA. But when the same phage contained any type of mutated A gene, the percentage of DNA packaged decreased dramatically. complete
CACAO 13561
on LAMBD:TERL
Flagged
Public
Assessment		Ivanerill2019-03-25 16:30:28 CDT

Move Annotation 13561 from 9CAUD:A0A2D1GP30 to LAMBD:TERL

Updated by Instructor
Public
Assessment		Ivanerill2019-03-13 09:23:55 CDT

The protein is SEA_ABT2GRADUATEX2_3, and the paper about lambda terminase. The GO is also wrong, since it's cellular location and table 5 does not go into localization of the protein. The evidence term is also wrong. Whatever they conclude about the terminase protein is not due to direct assay, but to a different type of experimental setup. Notes are nice, but not in tune with the other annotation fields.

Please use the cross-linked evidence terms from ECO (i.e. those that end in "used in manual assertion" or "used in automatic assertion") Most instances of evidence you will come across will be of type "used in manual assertion". Terms with "used in automatic assertion" imply that the authors did not make a conscious effort to analyze the results of an experiment, letting an algorithm make the call. For instance, if somebody were to use BLAST to determine that a bunch of proteins are homologous (and hence have the same function as the query) and they do not assess the BLAST results in any way (just accept whatever BLAST returns as significant given a preestablished threshold) that could be thought of as an "automatic assertion".


Requires Changes
✗ Protein
✔ Publication
✗ Go term
✗ Evidence
✗ Notes
Private
Assessment		Ivanerill2019-03-11 15:58:34 CDTYou need to be an instructor to view these notes.Requires Changes
✗ Protein
✔ Publication
✗ Go term
✗ Evidence
✗ Notes


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