2010 GO camp Use of Regulation issues

1. Background

David Hill's slides

2. Review of current GO annotation practices

Question 1: How do groups decide on when to annotate to 'regulates process x' or 'process x'? For instance does SLIT regulate axon guidance or involved in the process of axon guidance? Val - this depends on the defined start/end of a process and somethings can be annotated to BOTH the regulates term and also directly to the process term. Some groups decide that if removing the activity of a gene product produces an all/nothing event - then they define it as being part of the process. When should annotations be inherited up the regulates relationship?

Question 2: Annotations could be checked more efficiently if GO term definitions could include the beginning and end of a process.

Question 3 (from Ruth): Should we also consider how the 'activity' of a protein is defined when making these regulation/process decisions. The definition for transcription factor activity is: The function of binding to a specific DNA sequence in order to modulate transcription.... This suggests that a transcription factor is involved in the process of regulating transcription rather than involved in the process of transcription itself. However, some of us in the UK feel that many transcription factors are involved in the transcription process itself definition: The synthesis of either RNA on a template of DNA or DNA on a template of RNA. Does the definition for transcription factor activity need modification to enable this annotation, or are only the polymerases involved in the synthesis?)

Question 3: Regulation of processes, especially with IMP;

• example 1: [1]

4. Examples (papers) and discussion of GO annotation issues

1. (from Rachael): PMID:19424712 - Ang1 is the ligand for TIE2, so it activates TIE2 which is then internalized and degraded. (Fig. 5a) HUVECs were incubated with Ang1 and the amount of Tie2 remaining at cell surface was decreased, therefore it has been internalized - question is whether Ang1 should be annotated to the process 'receptor internalization' or the regulation of? Or is GO:0007171 'activation of transmembrane receptor protein tyrosine kinase activity' enough?

1. (from Val) I queried with SGD why ATG1 was annotated to "autophagic vacuole assembly"rather than a "regulation of" (see 3 abstracts below). I think that the general conclusion was that the annotation was OK, because researchers considered that ATG1 was part of the autophagy process.

The general consensus was that this is an integral part of autophagy and the arguments for this were convincing.

This seems OK, but I still felt that something is missing. Maybe, if this is an example of where the definition of the process needs to be updated to say exactly which step is the beginning of the process. Not knowing much about this process, with these papers I know I would have annotated to "regulation of", mainly bacause it's a kinase and because of the use of "regulation" in the titles and abstracts by the authors.

Scott RC, et al.  (2007)  Direct induction of autophagy by Atg1 inhibits cell growth and induces apoptotic cell death. Curr Biol 17(1):1-11
Abstract
BACKGROUND: To survive starvation and other forms of stress, eukaryotic
cells undergo a lysosomal process of cytoplasmic degradation known as
autophagy. Autophagy has been implicated in a number of cellular and
developmental processes, including cell-growth control and programmed cell
death. However, direct evidence of a causal role for autophagy in these
processes is lacking, resulting in part from the pleiotropic effects of
signaling molecules such as TOR that regulate autophagy. Here, we
circumvent this difficulty by directly manipulating autophagy rates in
Drosophila through the autophagy-specific protein kinase Atg1. RESULTS: We
find that overexpression of Atg1 is sufficient to induce high levels of
autophagy, the first such demonstration among wild-type Atg proteins. In
contrast to findings in yeast, induction of autophagy by Atg1 is dependent
on its kinase activity. We find that cells with high levels of
Atg1-induced autophagy are rapidly eliminated, demonstrating that
autophagy is capable of inducing cell death. However, this cell death is
caspase dependent and displays DNA fragmentation, suggesting that
autophagy represents an alternative induction of apoptosis, rather than a
distinct form of cell death. In addition, we demonstrate that Atg1-induced
autophagy strongly inhibits cell growth and that Atg1 mutant cells have a
relative growth advantage under conditions of reduced TOR signaling.
Finally, we show that Atg1 expression results in negative feedback on the
activity of TOR itself. CONCLUSIONS: Our results reveal a central role for
Atg1 in mounting a coordinated autophagic response and demonstrate that
autophagy has the capacity to induce cell death. Furthermore, this work
identifies autophagy as a critical mechanism by which inhibition of TOR
signaling leads to reduced cell growth.

Evolution of Atg1 function and regulation. Chan EY, Tooze SA. Abstract The serine/threonine kinase Atg1 plays an essential role downstream of TOR for the regulation of autophagy. In yeast, where Atg1 was first identified, a complex regulatory mechanism has been described that includes at least seven other interacting proteins and a phosphorylation-dependent switch. Recent findings confirm that the mammalian Atg1 homologues ULK1 and 2 have autophagy regulatory roles. However, we and others have also demonstrated mechanistic differences with the yeast model and between these two Atg1 family members. Here, we elaborate on our growing understanding of Atg1 function, incorporating findings from yeast, C. elegans, D. melanogaster and mammalian cells. We propose that through evolution, Atg1 proteins have adopted additional cellular functions and regulatory mechanisms, which could involve multiple gene family isoforms working within multifunctional protein complexes. The gene family expansion observed in higher eukaryotes might reflect an increased functional diversity of Atg1 proteins in cell growth, differentiation and survival. PMID: 19411825

The role of the Atg1/ULK1 complex in autophagy regulation. Mizushima N. Department of Physiology and Cell Biology, Tokyo Medical and Dental University, Tokyo 113-8519, Japan. nmizu.phy2@tmd.ac.jp The Atg1/ULK complex plays an essential role in the initiation of autophagy: receiving signals of cellular nutrient status, recruiting downstream Atg proteins to the autophagosome formation site, and governing autophagosome formation. Recent studies of mammalian Atg1 homologs (ULK1 and ULK2) have identified several novel interacting proteins, FIP200, mAtg13, and Atg101. FIP200 and Atg101 are not conserved in Saccharomyces cerevisiae, despite the high conservation rates of other downstream Atg proteins between the yeast and mammals. Furthermore, through studies of the Atg1/ULK1 complex, the molecular mechanism by which (m)TORC1 regulates autophagy is now being clarified in detail. Copyright 2009 Elsevier Ltd. All rights reserved. PMID: 20056399

5. Suggestions for Quality Control procedures

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