POLA1 Curator Discussion (Retired)

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Quality control issues for polA1 annotations; Checked annotation summary graphs from 16.11.2007


Functions

  • Human gene is annotated to 'sugar binding' based on reactivity with conA. Is this correct?

Pascale 09:01, 25 January 2008 (PST)

- ConA is a lectin and it is this that does the sugar binding, therefore I have removed the annotation to PolA. (Rachael 6 February 2008)

  • How universal are some functions? (ie, can they safely be ISS'ed):
    • nucleotide binding
    • pyrimidine nucleotide binding
    • purine nt binding
    • chromatin binding
    • DNA binding
    • double stranded DNA binding

Pascale 09:01, 25 January 2008 (PST)

  • protein heterodimerization activity

Pascale 09:01, 25 January 2008 (PST)


For the following:

  • alpha DNA polymerase activity
  • alpha DNA primase activity

If the complex 'alpha DNA ploymerase:primase complex' is correct, you expect polA to have a role in both functions? And the corresponding processes.

Pascale 09:01, 25 January 2008 (PST)

Processes

  • Human gene is annotated to 'response to pH': in the original paper (PMID: 7504813), they demonstrated "that the fidelity of human DNA polymerase alpha increases 10-fold when the pH of the in vitro synthesis reaction is lowered from pH 8.6 to pH 6.1"

I think this annotation is wrong, and so are the two ISS (rat, chicken). Assaying enzyme activity at different pH measures a characteristic of the enzyme. The definition of 'response to pH is 'A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus'. In this case they assays the enzyme in vitro, thus no conclusion can be made about the cellular response. Pascale 09:03, 25 January 2008 (PST)

- Agreed, the annotations to 'response to pH' to human, rat and chicken have been removed. (Rachael 6 February 2008)


  • Human gene is annotated top 'response to virus'. From abstract of PMID: 1848671

"We observed that the synthesis of ribonucleotide primers by DNA polymerase alpha-primase is dramatically stimulated by SV40 T antigen. The presence of T antigen also increased the average length of the DNA product synthesized on primed and unprimed single-stranded DNA templates."
The annotation seems wrong: the V40 T antigen stimulates DNA replication; but not the other way around. Pascale 09:03, 25 January 2008 (PST)

- Agreed, the annotation to 'response to virus' has been removed from human. (Rachael 6 February 2008)

Components

  • alpha DNA ploymerase:primase complex (mouse, human, rat, fly, yeast, pombe) : Can this be applied to all other organisms?

Pascale 09:03, 25 January 2008 (PST)

Also, are the following expected to be universal? (some people have ISS'ed to those; I'd be comfortable to ISS to nucleus, but nothing more granular, unless there is evidence that those other components can reasonably be inferred for all eukaryotes>

  • chromatin
  • nucleoplasm
  • nuclear matrix
  • nucleolous

Pascale 09:03, 25 January 2008 (PST)

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