Additional MAP kinase cascades

[gocentral]

Additional MAP kinase cascades

In mammals there are at least four classes of MAPKKK cascades, the canonical "ERK" cascade involving ERK1/2 and the upstream kinases MEK1/2, the "JNK" cascade, involving the JNKs and the upstream kinases MKK4/7, the "p38" stress-activated cascade, involving the upstream kinases MKK3/MKK6, and the "big MAP kinase" cascade, involving BMK1/ERK5, and the upstream kinase MEK5.

However under the general term MAPKKK in the GO we only represent two of these four cascades, the JNK and p38 cascades: "JNK cascade ; GO:0007254" and "stress-activated MAPK cascade ; GO:0051403". There are several reasons for this, including the initial yeast focus of the MAP kinase terms, the confusion of nomenclature around all map kinase genes and pathways, lack of an expert in the field to revise this area, and general inertia. While I can hardly claim to be an expert here, I have now overcome my personal inertia to learning about this area in greater detail in order to provide a more complete representation of these cascades. This is going to help out in annotation particularly in providing an actual term to cover the common ERK1/2 cascade, which has been sorely lacking and the source of some confusion.

Thus I propose the following new terms:

MAPKKK cascade --< activation of MAPK activity + --< activation of MAPKK activity + --< activation of MAPKKK activity + --< inactivation of MAPK activity + --< inactivation of MAPKK activity --< inactivation of MAPKKK activity --% JNK cascade ; GO:0007254 --% MAPKKK cascade during cell wall biogenesis + --% MAPKKK cascade during osmolarity sensing + --R-negative regulation of MAPKKK cascade + --< nuclear translocation of MAPK + --R+positive regulation of MAPKKK cascade + --R regulation of MAPKKK cascade + --% stress-activated MAPK cascade ; GO:0051403 --% ERK cascade ; GO:NewTer1 ----< regulation of ERK cascade ; GO:NewTer2 ------% negative regulation of ERK cascade ; GO:NewTer2 ------% positive regulation of ERK cascade ; GO:NewTer3 --% BMK cascade ; GO:NewTer4 ----< regulation of BMK cascade ; GO:NewTer5 ------% negative regulation of BMK cascade ; GO:NewTer6 ------% positive regulation of BMK cascade ; GO:NewTer7

[Term] id: GO:NewTer1 name: ERK1 and ERK2 cascade namespace: biological_process def: "A cascade of protein kinase activities, culminating in the phosphorylation and activation of either the ERK1 or ERK2 kinases, which in turn are a subfamily of mitogen-activated protein (MAP) kinases." [GOC:add, ISBN:0121245462, ISBN:0896039986] comment: Note that this MAPKKK cascade is commonly refered to as the ERK pathway in the literature, but involves only ERK1 or ERK2, not other ERK kinases." synonym: "ERK1 cascade" NARROW synonym: "ERK2 cascade" NARROW synonym: "MAPK1 cascade" NARROW synonym: "MAPK3 cascade" NARROW synonym: "ERK1/2 cascade" EXACT synonym: "ERK cascade" BROAD is_a: GO:0000165 ! MAPKKK cascade

The regulation terms for this term are standard and should be reference to [GOC:add, ISBN:0121245462, ISBN:0896039986] as well. I trust whoever enters these terms will add all the appropriate relationships.

[Term] id: GO:NewTer2 name: BMK cascade namespace: biological_process def: "A cascade of protein kinase activities, culminating in the phosphorylation and activation of big MAP kinase (BMK1/ERK5), which is a type of mitogen-activated protein (MAP) kinases." [GOC:add, PMID:16376520. PMID:16880823, ISBN:0896039986] synonym: "BMK1 cascade" EXACT synonym: "ERK5 cascade" EXACT synonym: "MAPK7 cascade" EXACT synonym: "ERK5 signaling pathway" EXACT [PMID:16376520] is_a: GO:0000165 ! MAPKKK cascade

The regulation terms for this term are standard and should be reference to [GOC:add, PMID:16376520. PMID:16880823, ISBN:0896039986] as well. I trust whoever enters these terms will add all the appropriate relationships.

I would also like the following synonyms added:

[Term] id: GO:0007254 name: JNK cascade [existing synoynyms] synonym: "SAPK cascade" BROAD synonym: "stress-activated protein kinase cascade" BROAD [new synonyms] synonym: "JNK1 cascade" NARROW synonym: "MAPK8 cascade" NARROW synonym: "JNK2 cascade" NARROW synonym: "MAPK9 cascade" NARROW synonym: "JNK3 cascade" NARROW synonym: "MAPK10 cascade" NARROW

[Term] id: GO:0051403 name: stress-activated MAPK cascade [existing synoynyms] synonym: "p38 MAPK signaling" EXACT synonym: "p38 MAPK signalling" EXACT synonym: "stress-activated MAPK signaling pathway" EXACT synonym: "stress-activated MAPK signalling pathway" EXACT synonym: "stress-activated MAPKKK cascade" EXACT synonym: "stress-activated MAPKKK signaling pathway" EXACT synonym: "stress-activated MAPKKK signalling pathway" EXACT [new synonyms] synonym: "p38 cascade" NARROW synonym: "MAPK14 cascade" NARROW synonym: "MAPK11 cascade" NARROW synonym: "MAPK12 cascade" NARROW synonym: "MAPK13 cascade" NARROW synonym: "SAPK cascade" BROAD

Thanks,

Alex

Reported by: addiehl

Original Ticket: "geneontology/ontology-requests/5836":https://sourceforge.net/p/geneontology/ontology-requests/5836

[gocentral]

• labels: --> New term request
• milestone: --> MGI

Original comment by: addiehl

[gocentral]

added ERK1 and ERK2 cascade GO:0070371 regulation of ERK1 and ERK2 cascade GO:0070372 negative regulation of ERK1 and ERK2 cascade GO:0070373 positive regulation of ERK1 and ERK2 cascade GO:0070374 BMK cascade GO:0070375 regulation of BMK cascade GO:0070376 negative regulation of BMK cascade GO:0070377 positive regulation of BMK cascade GO:0070378

also added synonyms as requested; please check for errors as usual

m

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori
• status: open --> closed-accepted

Original comment by: mah11

[gocentral]

One error, my fault: Final word for definition of 'BMK cascade ; GO:0070375' should be 'kinase,' not 'kinases.'

Thanks,

Alex

Original comment by: addiehl

[gocentral]

typo fixed; thanks

Original comment by: mah11