#11686 Autophagy

[Marc Feuermann]

Organellar autophagy occurs through macroautophagy (engulfment by autophagosomes).
I suggest few name changes, and adding some references.

GO:0000422 mitochondrion degradation
Change name to 'mitophagy'
I would remove the term mitochondrial degradation which is confusing (so not as synonym). Definition is okay
ADD:
PMID:23065344
PMID:19289147
is_a: GO:0016236 ! macroautophagy
REMOVE:
is_a: GO:0006914 ! autophagy

GO:0044804 nucleophagy
Name and definition okay
ADD:
is_a: GO:0016236 ! macroautophagy
REMOVE:
is_a: GO:0006914 ! autophagy

GO:0044805 late nucleophagy
Name and definition okay
ADD:
is_a: GO:0016236 ! macroautophagy
REMOVE:
is_a: GO:0006914 ! autophagy

GO:0030242 peroxisome degradation
I would exchange name and synonym:
Name: pexophagy
Synonym: peroxisome degradation
ADD:
PMID:20083110
is_a: GO:0016236 ! macroautophagy
REMOVE:
is_a: GO:0006914 ! autophagy

GO:0034517 ribophagy
Name and definition okay
ADD:
is_a: GO:0016236 ! macroautophagy
REMOVE:
is_a: GO:0006914 ! autophagy

GO:0035973 aggrephagy
Name and definition okay
ADD:
PMID:25062811

GO:0098792 xenophagy
Name and definition okay
ADD:
PMID:25497060

[Paul Denny]

At the Warwick Autophagy meeting, these processes were mentioned - should we contemplate new terms for these, too?
reticulophagy (targeted autophagy of ER - 8 papers in Pubmed)
glycophagy (targeted autophagy of glycogen - 5 papers in Pubmed)
lipophagy (targeted autophagy of lipids - 38 papers in Pubmed)
The speaker didn't go into details or mention specific proteins involved in any of these, so perhaps this is premature. I have emailed him for his opinion.

[Paola Roncaglia]

Discussed at the second meeting:
- nucleophagy must be kept directly under autophagy
- late nucleophagy needs more reading
- in general, look carefully at parentage and def, because not everything might go under macroautophagy

[Paul Denny]

Recent review found after second meeting (19th May)
PMID: 25009776
Discusses three types of mitophagy:
•In Type 1 mitophagy, cup-shaped phagophores engulf mitochondria during starvation.
•In Type 2 mitophagy, autophagic membranes coalesce around damaged mitochondria.
•Type 1 but not Type 2 mitophagy requires PI3K and occurs with mitochondrial fission.
•Multivesicular bodies engulf mitochondria-derived vesicles in Type 3 micromitophagy.
Type 1 sounds like classic macroautophagy, but targeted at mitochondrion.
I think we need to take this into account when rebuilding the ontology.

[Marc Feuermann]

We've found specific receptors for reticulophagy in two recent Nature papers. So I think we can create the corresponding term: reticulophagy (which seems to be part of macroautophagy)

Biological Process
Definition: The autophagic process in which the endoplasmic reticulum is delivered to the vacuole and degraded in response to changing cellular conditions.

PMID:26040717
PMID:24060720

Synomym: ER-phagy

is_a: GO:0016236 ! macroautophagy

[David Hill]

[Term]
+id: GO:0061709
+name: reticulophagy
+namespace: biological_process
+def: "The autophagic process in which the endoplasmic reticulum is delivered to the vacuole and degraded in response to changing cellular conditions." [GOC:autophagy, GOC:dph, PMID:24060720, PMID:26040717]
+synonym: "ER-phagy" EXACT []
+is_a: GO:0016236 ! macroautophagy
+created_by: dph
+creation_date: 2015-06-18T15:15:48Z

[David Hill]

Turns out 'endoplasmic reticulum degradation' was added to the ontology previously and is the same process. I merged the two terms. Here is the diff.

id: GO:0061709
name: reticulophagy
namespace: biological_process
-def: "The autophagic process in which the endoplasmic reticulum is delivered to the vacuole and degraded in response to changing cellular conditions." [GOC:autophagy, GOC:dph, PMID:24060720, PMID:26040717]
+alt_id: GO:1990766
+def: "The autophagic process in which parts of the endoplasmic reticulum are loaded into autophagosomes, delivered to the vacuole, and degraded in response to changing cellular conditions." [GOC:autophagy, GOC:dph, PMID:22481944, PMID:24060720, PMID:26040717]
+synonym: "autophagy of the endoplasmic reticulum" EXACT []
+synonym: "autophagy of the ER" EXACT []
+synonym: "endoplasmic reticulum degradation" RELATED []
+synonym: "ER degradation" RELATED []
synonym: "ER-phagy" EXACT []
is_a: GO:0016236 ! macroautophagy
+is_a: GO:1903008 ! organelle disassembly
created_by: dph
creation_date: 2015-06-18T15:15:48Z

@@ -584342,22 +584350,6 @@
creation_date: 2015-06-10T18:29:21Z

[Term]
-id: GO:1990766
-name: endoplasmic reticulum degradation
-namespace: biological_process
-def: "The autophagic process in which parts of the endoplasmic reticulum are loaded into autophagosomes, delivered to the vacuole, and degraded in response to changing cellular conditions." [PMID:26040717]
-synonym: "autophagy of the endoplasmic reticulum" EXACT []
-synonym: "autophagy of the ER" EXACT []
-synonym: "ER degradation" EXACT []
-synonym: "ER-phagy" EXACT []
-synonym: "reticulophagy" EXACT [PMID:22481944]
-is_a: GO:0006914 ! autophagy
-is_a: GO:0044712 {is_inferred="true"} ! single-organism catabolic process
-is_a: GO:1903008 ! organelle disassembly
-created_by: mcc
-creation_date: 2015-06-10T18:25:51Z

[Marc Feuermann]

I've found at least one protein involved directly in glycophagy. Human STBD1 seems to be a cargo receptor for glycogen that delivers its cargo to an autophagic pathway resulting in the transport of glycogen to lysosomes. It binds to ATG8-like proteins, so the process is a macroautophagic process. I propose to create the term:

Glycophagy
Biological Process
Definition: The autophagic process in which cellular glycogen is delivered to the vacuole and degraded in response to changing cellular conditions.

PMID:21893048

is_a: GO:0016236 ! macroautophagy

Thanks,
Marc.

[Paul Denny]

Interesting - thanks Marc. This protein is encoded by a Parkinson's disease risk candidate gene, identified in GWAS
PMID:21738488

[Marc Feuermann]

To complete the terms, PMID:23708524 shows that mammalian ADRB2 and RAB7A are involved in the positive regulation of lipophagy. RAB7A could even be a lipid droplet receptor for lipophagy. Again the process goes through autophagosomes, so it is macroautophagy. So I think we can create this term too (as well as the corresponding regulatory terms: 'regulation of', 'positive regulation of' and 'negative regulation of'):

lipophagy
Biological Process
Definition: The autophagic process in which lipid droplets are delivered to the vacuole and degraded in response to changing cellular conditions.

PMID:26076903
PMID:23708524

is_a: GO:0016236 ! macroautophagy

Thanks a lot.
Marc.

[Marc Feuermann]

Some more information about lipid degradation:
There are two types of lipid degradation pathways (lipid catabolic processes).
1-Cytosolic lipolysis: breakdown of lipid droplets and hydrolysis of stored triglycerids occur through the orchestrated activation of cytosolic lipases mediated by hormones.
2- Autophagy-mediated lysosomal lipid degradation (lipophagy). lipid droplets are delivered to the vacuole though the autophagosome.

Regards,
Marc.

[David Hill]

OK. I think I have covered everything here. Here is a partial diff, omitting any changes to the names of regulation terms etc. Please let me know if you spot errors or omissions.

-D

[Term]
id: GO:0000422
-name: mitochondrion degradation
+name: mitophagy
namespace: biological_process
-def: "The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions." [PMID:15798367]
-synonym: "mitophagy" EXACT []
+def: "The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions." [GOC:autophagy, PMID:15798367, PMID:19289147, PMID:23065344]
+synonym: "mitochondrion autophagy" EXACT [GOC:autophagy]
xref: Wikipedia:Autophagy_(cellular)#Selective_autophagy
xref: Wikipedia:Mitophagy
-is_a: GO:0006914 ! autophagy
is_a: GO:0007005 {is_inferred="true"} ! mitochondrion organization
-is_a: GO:0044712 {is_inferred="true"} ! single-organism catabolic process
+is_a: GO:0016236 ! macroautophagy
is_a: GO:1903008 {is_inferred="true"} ! organelle disassembly
relationship: results_in_disassembly_of GO:0005739 ! mitochondrion

[Term]
id: GO:0030242
-name: peroxisome degradation
+name: pexophagy
namespace: biological_process
-def: "The process in which peroxisomes are delivered to the vacuole and degraded in response to changing nutrient conditions." [PMID:10547367]
-synonym: "pexophagy" EXACT []
-is_a: GO:0006914 ! autophagy
+def: "The process in which peroxisomes are delivered to the vacuole and degraded in response to changing nutrient conditions." [GOC:autophagy, PMID:10547367, PMID:20083110]
+synonym: "peroxisome degradation" BROAD []
is_a: GO:0007031 ! peroxisome organization
+is_a: GO:0016236 ! macroautophagy
is_a: GO:0044712 {is_inferred="true"} ! single-organism catabolic process
is_a: GO:1902589 {is_inferred="true"} ! single-organism organelle organization

id: GO:0034517
name: ribophagy
namespace: biological_process
-def: "The process in which cells degrade mature ribosomes under conditions of starvation." [PMID:18391941]
-is_a: GO:0006914 ! autophagy
+def: "The process in which cells degrade mature ribosomes under conditions of starvation." [GOC:autophagy, PMID:18391941]
+is_a: GO:0016236 ! macroautophagy

[Term]
id: GO:0035695
-name: mitochondrion degradation by induced vacuole formation
+name: mitophagy by induced vacuole formation
namespace: biological_process
-def: "The process in which cells degrade mitochondria by inducing a vacuole-like structure which directly engulfs and degrades the unhealthy mitochondria by accumulating lysosomes." [GOC:bf, GOC:sp, PMID:21264228]
+def: "The process in which cells degrade mitochondria by inducing a vacuole-like structure which directly engulfs and degrades the unhealthy mitochondria by accumulating lysosomes." [GOC:autophagy, GOC:bf, GOC:sp, PMID:21264228]
comment: In this mechanism of mitochondrion degradation, the mitochondrion is directly engulfed by a lysosome-like vacuole. It is therefore distinct from canonical autophagy, which is mediated by a double-membrane autophagosome.
synonym: "MIV-mediated mitophagy" NARROW [PMID:21264228]
-is_a: GO:0000422 ! mitochondrion degradation
+is_a: GO:0000422 ! mitophagy
created_by: rfoulger
creation_date: 2011-02-28T03:01:04Z

name: aggrephagy
namespace: biological_process
alt_id: GO:0035972
-def: "Selective degradation of protein aggregates by macroautophagy." [GOC:kmv, PMID:18508269]
+def: "Selective degradation of protein aggregates by macroautophagy." [GOC:autophagy, GOC:kmv, PMID:18508269, PMID:25062811]
is_a: GO:0016236 ! macroautophagy
created_by: rfoulger
creation_date: 2011-08-09T09:53:40Z

[Term]
+id: GO:0061723
+name: glycophagy
+namespace: biological_process
+def: "The autophagic process in which cellular glycogen is delivered to the vacuole and degraded in response to changing cellular conditions." [PMID:21893048]
+is_a: GO:0016236 ! macroautophagy
+created_by: dph
+creation_date: 2015-07-08T13:36:51Z

+[Term]
+id: GO:0061724
+name: lipophagy
+namespace: biological_process
+def: "The autophagic process in which lipid droplets are delivered to the vacuole and degraded in response to changing cellular conditions." [GOC:autophagy, PMID:23708524, PMID:26076903]
+is_a: GO:0016236 ! macroautophagy
+is_a: GO:0044242 ! cellular lipid catabolic process
+created_by: dph
+creation_date: 2015-07-08T13:38:19Z
+
+[Term]
+id: GO:0061725
+name: cytosolic lipolysis
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the breakdown of lipid droplets and hydrolysis of stored triglycerides occurring through the orchestrated activation of cytosolic lipases." [GOC:autophagy]
+is_a: GO:0044242 ! cellular lipid catabolic process
+intersection_of: GO:0009056 ! catabolic process
+intersection_of: has_input CHEBI:18059 ! lipid
+intersection_of: occurs_in GO:0005829 ! cytosol
+created_by: dph
+creation_date: 2015-07-08T13:42:15Z