YGR157W - Revision history

Timlevine at 16:17, 21 March 2013

2013-03-21T16:17:32Z

Timlevine at 15:56, 21 March 2013

2013-03-21T15:56:17Z

Timlevine at 15:39, 21 March 2013

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Timlevine at 11:23, 25 August 2011

2011-08-25T11:23:39Z

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‎Community Commentary

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← Older revision		Revision as of 16:17, 21 March 2013
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−	==	+	== Cho2 - domain structure and involvement in autophagy via Atg8p / LC3 ==
−	Cho2 - domain structure and involvement in autophagy via Atg8p / LC3 ==

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 (3) Wlodarski et al. suggest that DWIGLYKV in Cho2p interacts with transcriptional activators related to p300, and so Cho2p is active in chromatic remodelling. However, there is little evidence to support this. Yang et al. <ref name='PMID 16931570'> Yang CK, Kim JH and Stallcup MR (2006) Role of the N-terminal activation domain of the coiled-coil coactivator in mediating transcriptional activation by beta-catenin. Mol Endocrinol. 2006 Dec;20(12):3251-62. PMID 16931570</ref> showed that the motif in CoCoa_N that binds to p300 is FLNVARTY, not DWIGLYKV which is >20 aa away. Also, Cho2p has no conserved sequence motif similar to FLNVARTY.
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← Older revision		Revision as of 15:39, 21 March 2013
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	==		==
−	Cho2 - domain structure and involvement in autophagy via Atg8p / LC3 ==	+	Cho2 - domain structure and involvement in autophagy via Atg8p / LC3 ==

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 {|{{Prettytable}} align = 'right' width = '200px'
 |-
-|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Systematic name''' || [http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=S000003389 YGR157W]
+|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Systematic name''' || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000003389 YGR157W]
 |-
 |valign="top" nowrap bgcolor="{{SGDblue}}"| '''Gene name'''         ||''CHO2 ''

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 ==References==
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-Wlodarski et al (2011) (www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0023168) have identified a CoCoa_N domain at the carboxy-terminus of Cho2p. This is interesting, but not precisely for the reasons stated by Wlodarski et al., as explained below. Point (1) refers to the domain structure of Cho2p and points (2) and (3) provide an alternative likely function (and hence alternative binding partner) for a conserved motif in the carboxy-terminus of Cho2p to that suggested by Wlodarski et al.
+Wlodarski et al <ref name='PMID 21858014'> Wlodarski T, Kutner J, Towpik J, Knizewski L, Rychlewski L, Kudlicki A, Rowicka M, Dziembowski A and Ginalski K (2011) Comprehensive Structural and Substrate Specificity Classification of the Saccharomyces cerevisiae Methyltransferome. PLoS One. 2011;6(8):e23168. Epub 2011 Aug 9. PMID 21858014</ref> have identified a CoCoa_N domain at the carboxy-terminus of Cho2p. This is interesting, but not precisely for the reasons stated by Wlodarski et al., as explained below. Point (1) refers to the domain structure of Cho2p and points (2) and (3) provide an alternative likely function (and hence alternative binding partner) for a conserved motif in the carboxy-terminus of Cho2p to that suggested by Wlodarski et al.
 (1) The enzymatic domain of Cho2p is repeated, as residues 35-321 are homologous to 344-577. This means that the whole amino-terminus 1-577 most likely contains an even number of transmembrane domains, despite automated prediction programmes suggesting an overall odd number. This is important because it sugests that the carboxy-terminus is in the cytoplasm (not in the lumen as might be assumed from Wlodarski et al.)
-(2) the C-terminus of Cho2p contains WIGL. This motif is not only found in CoCoa_N, but also is found in the SKICH domains of phosphatidylinositol (4,5) bisphosphate 5-phosphatase (PIPP) and other proteins (Ooms et al. (2006) MBoC 17, 607-22).
+(2) the C-terminus of Cho2p contains WIGL. This motif is not only found in CoCoa_N, but also is found in the SKICH domains of phosphatidylinositol (4,5) bisphosphate 5-phosphatase (PIPP) and other proteins <ref name='PMID 16280363'> Ooms LM, Fedele CG, Astle MV, Ivetac I, Cheung V, Pearson RB, Layton MJ, Forrai A, Nandurkar HH, Mitchell CA (2006) The inositol polyphosphate 5-phosphatase, PIPP, Is a novel regulator of phosphoinositide 3-kinase-dependent neurite elongation. Mol Biol Cell. 17(2):607-22. PMID 16280363</ref>.
-Critically the motif is of the form '''WxxL''', which is the minimal requirement for motifs binding to Atg8/LC3 (Noda et al. (2010) FEBS Letters 584:1379–85). WxxL motifs tend to have two other features also found in Cho2p: (A) they form beta-sheets, which is the structure for this portion of Cho2p predicted by PSI-PRED 3.0 (B) they are flanked by acidic residues (here in Cho2p: DDwiglYKVID). Together these factors create the strong suggestion that WIGL near the carboxy-terminus of Cho2p binds to Atg8p/LC3. Hence, it is predicted that Cho2p is directly involved in autophagy, possibly by methylating phosphatidylethanolamine, which is specifically required to activate Atg8p/LC3.
+Critically the motif is of the form '''WxxL''', which is the minimal requirement for motifs binding to Atg8/LC3 <ref name='PMID 20083108'> Noda NN, Ohsumi Y and Inagaki F (2010) Atg8-family interacting motif crucial for selective autophagy. FEBS Lett. 584(7):1379-85. PMID 20083108</ref>. WxxL motifs tend to have two other features also found in Cho2p: (A) they form beta-sheets, which is the structure for this portion of Cho2p predicted by PSI-PRED 3.0 (B) they are flanked by acidic residues (here in Cho2p: DDwiglYKVID). Together these factors create the strong suggestion that WIGL near the carboxy-terminus of Cho2p binds to Atg8p/LC3. Hence, it is predicted that Cho2p is directly involved in autophagy, possibly by methylating phosphatidylethanolamine, which is specifically required to activate Atg8p/LC3.
-(3) Wlodarski et al. suggest that DWIGLYKV in Cho2p interacts with transcriptional activators related to p300, and so Cho2p is active in chromatic remodelling. However, there is little evidence to support this. Yang et al. (2006, Mol Endocrinol. 20: 3251-62) showed that the motif in CoCoa_N that binds to p300 is FLNVARTY, not DWIGLYKV which is >20 aa away. Also, Cho2p has no conserved sequence motif similar to FLNVARTY.
+(3) Wlodarski et al. suggest that DWIGLYKV in Cho2p interacts with transcriptional activators related to p300, and so Cho2p is active in chromatic remodelling. However, there is little evidence to support this. Yang et al. <ref name='PMID 16931570'> Yang CK, Kim JH and Stallcup MR (2006) Role of the N-terminal activation domain of the coiled-coil coactivator in mediating transcriptional activation by beta-catenin. Mol Endocrinol. 2006 Dec;20(12):3251-62. PMID 16931570</ref> showed that the motif in CoCoa_N that binds to p300 is FLNVARTY, not DWIGLYKV which is >20 aa away. Also, Cho2p has no conserved sequence motif similar to FLNVARTY.

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 |valign="top" nowrap bgcolor="{{SGDblue}}"| '''Coordinates'''
-|nowrap| Chr VII:802445..805054
+|nowrap| Chr VII:802440..805049
 |-
 |valign="top" nowrap bgcolor="{{SGDblue}}"| '''Primary SGDID'''           || S000003389

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 |}
 <br>
-'''Description of YGR157W:''' Phosphatidylethanolamine methyltransferase (PEMT), catalyzes the first step in the conversion of phosphatidylethanolamine to phosphatidylcholine during the methylation pathway of phosphatidylcholine biosynthesis<ref name='S000042469'>Kodaki T and Yamashita S (1987) Yeast phosphatidylethanolamine methylation pathway. Cloning and characterization of two distinct methyltransferase genes. J Biol Chem 262(32):15428-35 {{SGDpaper|S000042469}} PMID 2445736</ref><ref name='S000053915'>Summers EF, et al. (1988) Saccharomyces cerevisiae cho2 mutants are deficient in phospholipid methylation and cross-pathway regulation of inositol synthesis. Genetics 120(4):909-22 {{SGDpaper|S000053915}} PMID 3066687</ref><ref name='S000058496'>Paltauf F, et al. (1992) Regulation and compartmentalization of lipid synthesis in yeast. Pp. 415-500 in The Molecular and Cellular Biology of the Yeast Saccharomyces: Gene Expression, edited by Jones EW, Pringle JR and Broach JR. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press
+'''Description of YGR157W:''' Phosphatidylethanolamine methyltransferase (PEMT), catalyzes the first step in the conversion of phosphatidylethanolamine to phosphatidylcholine during the methylation pathway of phosphatidylcholine biosynthesis<ref name='S000042469'>Kodaki T and Yamashita S (1987) Yeast phosphatidylethanolamine methylation pathway. Cloning and characterization of two distinct methyltransferase genes. J Biol Chem 262(32):15428-35 {{SGDpaper|S000042469}} PMID 2445736</ref><ref name='S000058496'>Paltauf F, et al. (1992) Regulation and compartmentalization of lipid synthesis in yeast. Pp. 415-500 in The Molecular and Cellular Biology of the Yeast Saccharomyces: Gene Expression, edited by Jones EW, Pringle JR and Broach JR. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press {{SGDpaper|S000058496}} PMID </ref><ref name='S000053915'>Summers EF, et al. (1988) Saccharomyces cerevisiae cho2 mutants are deficient in phospholipid methylation and cross-pathway regulation of inositol synthesis. Genetics 120(4):909-22
-  {{SGDpaper|S000058496}} PMID </ref>
+  {{SGDpaper|S000053915}} PMID 3066687</ref>
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