Processing Function Terms Amelia Ireland. Function Problems Function-process crossover Function and...
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Transcript of Processing Function Terms Amelia Ireland. Function Problems Function-process crossover Function and...
Processing Function Terms
Amelia Ireland
Function Problems
• Function-process crossover Function and process are not orthogonal Functions appear in process and vice versa
• The ‘One Step Rule’ ‘Steps’ vary between terms
• ‘Clean’ and ‘dirty’ functions Many functions don’t fit the def ‘elemental activities describing the actions of a gene product at the molecular level’
• GO function is not what people mean when they talk about the ‘function of a protein’
The Proposal
• Move function terms representing steps in a process into the process ontology
Function Problems
• Function-process crossover Function and process are not orthogonal Functions appear in process and vice versa
• The ‘One Step Rule’ ‘Steps’ vary between terms
• ‘Clean’ and ‘dirty’ functions Many functions don’t fit the def ‘elemental activities describing the actions of a gene product at the molecular level’
• GO function is not what people mean when they talk about the ‘function of a protein’
The Process-Function Crossover
• Functions in process Detection
The series of events in which a stimulus type stimulus is received by a cell and converted into a molecular signal.
i.e. binding during a signaling pathway
Metabolism The chemical reactions involving xxx binding is a chemical reaction chemical reactions ‘involving’ xxx limits metabolism to reactions in which X is the product or those where X is the reactant, i.e. one step reactions
Many terms under ‘protein modification’
The Function-Process Crossover
• Processes in function ent-kaurene oxidase activity,
1.14.13.78 Catalysis of three successive oxidations
of the 4-methyl group of ent-kaurene resulting in kaurenoic acid.
1. ent-kaur-16-ene + NADPH + O2 = ent-kaur-16-en-19-ol + NADP+ + H2O
2. ent-kaur-16-en-19-ol + NADPH + O2 = ent-kaur-16-en-19-al + NADP+ + 2 H2O
3. ent-kaur-16-en-19-al + NADPH + O2 = ent-kaur-16-en-19-oate + NADP+ + H2O
The Process-Function Crossover
• Identical processes and functions histone H3-K4 methylation The modification of histone H3 by addition of a methyl group to lysine at position 4 of the histone.
histone lysine N-methyltransferase activity (H3-K4 specific)
Catalysis of the addition of a methyl group onto lysine at position 4 of the histone H3 protein.
Function Problems
• Function-process crossover Function and process are not orthogonal Functions appear in process and vice versa
• The ‘One Step Rule’ ‘Steps’ vary between terms
• ‘Clean’ and ‘dirty’ functions Many functions don’t fit the def ‘elemental activities describing the actions of a gene product at the molecular level’
• GO function is not what people mean when they talk about the ‘function of a protein’
The ‘One Step’ Rule
• Currently use the ‘one step rule’ to decide between process and function One step --> function More than one step --> process
• But what level should the ‘steps’ be at?
The ‘One Step’ Rule
One step… or many?
fructose-bisphosphate aldolase activity
http://www.bu.edu/aldolase/lab/aldolase/intro/mechanism.html
The ‘One Step’ Rule
glycerol-3-phosphate transporter activity
http://student.biology.arizona.edu/honors2004/group02/home02.html
(1) an inorganic phosphate (Pi) from the periplasm binds to Co; (2) the Co pore increases in diameter; (3) a G3P binds to the Co and brings the enlarged Co pore to normal size; (4) the Co pore continues to decrease in diameter until it closes completely, which forces the G3P to the cytoplasmic end where it attaches to the Ci end; (5) the Ci pore enlarges to a certain point; (6) the Ci pore decreases in size and forces a Pi out of the cytoplasm.
One step… or many?
Function Problems
• Function-process crossover Function and process are not orthogonal Functions appear in process and vice versa
• The ‘One Step Rule’ ‘Steps’ vary between terms
• ‘Clean’ and ‘dirty’ functions Many functions don’t fit the def ‘elemental activities describing the actions of a gene product at the molecular level’
• GO function is not what people mean when they talk about the ‘function of a protein’
Clean and Dirty Functions
• molecular function Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
• Two kinds of function term “Clean”: steps in a process “Dirty”: combination of two or more process, function or other attributes
‘Clean’ Functions
arginine catabolism to glutamate ; GO:0019544
arginase activity GO:0004053
ornithine-oxo-acid transaminase
activity GO:0004587
1-pyrroline-5-carboxylate
dehydrogenase activity GO:0003842
MetaCyc:ARGASEDEG-PWY arginine degradation I (arginase pathway)
arginine catabolism to glutamate
arginase activity
ornithine-oxo-acid transaminase activity
1-pyrroline-5-carboxylate dehydrogenase activity
‘Clean’ Functions
Notch signaling pathway ; GO:0007219
Notch binding ; GO:0005112
Delta binding ; GO:new
Notch receptor processingGO:0007220 (process term)
Notch signaling pathway
Delta binding
Notch binding
Notch receptor processing
‘Dirty’ Functions
• Not steps in a process• Represent a combination of two or more attributes from function, component, process or other domain
• May be occurrents (events) or continuants (entities)
‘Dirty’ Functions
• transcription factor activity Any activity required to initiate or regulate transcription; includes the actions of both gene regulatory proteins as well as the general transcription factors.
i.e. a role in regulation of transcription or transcription initiation
• receptor activity Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
i.e. binding in a signaling pathway
‘Dirty’ Functions
• ‘structural molecule activity’, ‘enzyme regulator activity’, ‘hormone activity’, ‘protein tag’ have similar problems
• Dirty functions represent a role or a class and cannot be linked to process terms using existing GO relationships
Function Problems
• Function-process crossover Function and process are not orthogonal Functions appear in process and vice versa
• The ‘One Step Rule’ ‘Steps’ vary between terms
• ‘Clean’ and ‘dirty’ functions Many functions don’t fit the def ‘elemental activities describing the actions of a gene product at the molecular level’
• GO function is not what people mean when they talk about the ‘function of a protein’
Proposed Solution
• Move terms representing events into the process ontology
Catalytic activities
• Terms would be rehomed under ‘metabolism’
metabolism hydrolase activity isomerase activity ligase activity lyase activity oxidoreductase activity transferase activity
Catalytic activities
• Individual reactions could be organised according to substances involved
arginine metabolism arginine biosynthesis
argininosuccinate lyase activity D-nopaline dehydrogenase activity
arginine catabolism arginase activity arginine 2-monooxygenase activity
Catalytic activities
• Reactions could be put into pathways
arginine catabolism arginase catabolism to glutamate
1-pyrroline-5-carboxylate dehydrogenase activity
arginase activity ornithine-oxo-acid transaminase activity
• Data from MetaCyc, FIGS, KEGG?
Catalytic activities
• Reactions in more than one pathway
arginase activity arginase activity during arginine catabolism to glutamate
arginase activity during arginine catabolism to pyruvate
Binding
• Binding terms could be rehomed under ‘metabolism’
metabolism amine metabolism
amine binding binding
amine binding
Binding
• Binding terms can now be linked with signaling pathways and other processes
Notch signaling pathway Notch binding during Notch signaling pathway Delta binding during Notch signaling pathway Notch receptor processing
…and the rest
• Transporter activity xxx transporter activity --> xxx transport
xxx permease activity --> permease-mediated xxx transport
• Receptor activity ligand binding during signaling pathway
• Regulator activity regulation
…and the rest
• Reinstate some obsoletes Cell adhesion molecule --> cell adhesion receptor binding during cell-cell adhesion
Synonyms
• All moved terms will be given many synonyms in both process and function ‘style’ e.g. glucose dehydrogenase, glucose dehydrogenation
glucose carrier, carrier-mediated glucose transport
Brave New Function World
• Redefine function Various dictionary definitions of function: the special, normal, or proper physiologic activity of a gene product
the actions and activities assigned to or required or expected of a gene product
what a gene product is used for the purpose, role, or function a gene product serves
The purpose or role a gene product serves in the normal physiologic activity of an organism. A gene product may have one or more functions.
Proposed Solution
• Keep ‘dirty’ terms representing combinations of function, process or other information in function
• New function def would allow us to add useful terms currently not allowed toxin ligand other suggestions?
Brave New Function World energy transducer enzyme motor nutrient reservoir signal
chemoattractant chemorepellant hormone ligand morphogen protein tag
structural molecule receptor regulator
chaperone regulator enzyme regulator transcription regulator translation regulator
transporter toxin
Processed Functions
Notch signaling pathway ; GO:0007219
Process: Notch binding ; GO:0005112function: ligand
process: Delta binding ; GO:newfunction: receptor
Processed Functions
arginine catabolism to glutamate ; GO:0019544
arginase activityenzyme
ornithine-oxo-acid transaminase
activityenzyme
1-pyrroline-5-carboxylate
dehydrogenase activity enzyme
MetaCyc:ARGASEDEG-PWY arginine degradation I (arginase pathway)
Pros and Cons
+ reactions involving a certain substrate can all be homed underneath ‘xxx metabolism’
+ reactions can be linked to pathways+ greater precision in annotation+ ontologies more consistent and ‘pure’
+ less redundancy between process and function
+ GO function closer to colloquial interpretation
Pros and Cons
- some adjustment needed by those accustomed to seeing binding and enzymatic reactions in function
- may take some time to implement- no obsoletions