PMID:26412237

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Figure in Paper Evidence Sentence(s) Gene or Protein WPO Annotation EQ Annotation GO Annotation Comments
Figure S1 ULP-2, a member of the Ulp2-like branch of SUMO proteases (Mukhopadhyay and Dasso, 2007) shares 17% amino acid similarity with the mammalian SUMO proteases SENP6 and SENP7 (Figure S1). ULP-2 n/a n/a MF - GO:0016929 SUMO-specific protease activity

BP - GO:0016926 protein desumoylation EC = ISS with human SENP6

Note that WB and UniProtKB both only represent the larger isoform right now.
Figure 1A-C, 1D and 1E RT-PCR of embryonic mRNA identified two ulp-2 isoforms; ulp-2a, which is expressed in both the nucleus and cytosol, and the shorter isoform ulp-2b, which is expressed solely in the cytosol (Figures 1D and 1E). UPL-2 n/a n/a CC - GO:0005634 nucleus

CC - GO:0005829 cytosol

EC = IDA

Note that WB and UniProtKB both only represent the larger isoform right now.
Figure 2, Figure S2 Embryos in which ulp-2 expression was silenced by RNAi or gene mutation—ulp-2(tv380), which we generated by the CRISPR/Cas9 system (Friedland et al., 2013)—were arrested (29% and 63.4% embryonic arrest, respectively) during a developmental window from late gastrulation through epidermal morphogenesis. ulp-2 embryonic arrest (WBPhenotype:0000867) embryo Ce (WBls:0000003); abnormal (PATO:0000460),

embryo development (GO:0009790); abnormal (PATO:0000460)

BP - GO:0009792 embryo development ending in birth or egg hatching

EC = IMP

Note that BP - GO:0009790 embryo development is included in the 'do not manually annotate' subset of GO terms
Figure 2, Figure S2 Arrested embryos were segregated into three major classes: (I) late gastrulation failure, (II) cleft/enclosure failure, and (III) elongation failure (Figure 2; Figure S2; Movies S1, S2, S3 and S4). ulp-2 embryonic arrest (WBPhenotype:0000867), gastrulation variant (WBPhenotype:0000047), ventral closure defective (WBPhenotype:0001908), embryo Ce (WBls:0000003); abnormal (PATO:0000460),

gastrulation (GO:0007369); non-functional (PATO:0001511), embryo development (GO:0009790); abnormal (PATO:0000460)

BP - GO:0007369 gastrulation

BP - GO:0010172 embryonic body morphogenesis

BP - GO:0016331 morphogenesis of embryonic epithelium

EC = IMP

Currently, there are not specific GO BP terms for late gastrulation, ventral cleft closure, ventral enclosure, embryonic and/or epidermal elongation.
Figure 2 Figure 2. ULP-2 KD Causes Dorsal Intercalation, Ventral Cleft Closure, and Epidermal Enclosure Defects in ulp-2(RNAi) Embryos ulp-2 BP - GO:0010172 embryonic body morphogenesis

BP - GO:0016331 morphogenesis of embryonic epithelium

EC = IMP

There is no specific GO BP term for dorsal intercalation.

Also, it would be helpful to define exactly when gastrulation begins and ends in C. elegans. Begins when two E daughters, Ea and Ep, start to ingress? Ends at ventral cleft closure?

Figure 2C Arrested embryos (29 ± 1.8% of total; n = 940) segregated into three major classes. Class I embryos were arrested at late gastrulation prior to the formation of epidermal cells. Cells in these embryos appeared round and detached, suggesting severe weakening of cell-cell adhesion. ulp-2 gastrulation variant (WBPhenotype:0000047), ventral closure defective (WBPhenotype:0001908), body elongation defective (WBPhenotype:0000242) embryo Ce(WBls:0000003); abnormal (PATO:0000460),

gastrulation (GO:0007369); non-functional (PATO:0001511), embryo development (GO:0009790); abnormal (PATO:0000460)

BP - GO:0007369 gastrulation

BP - GO:0070587 regulation of cell-cell adhesion involved in gastrulation

EC = IMP

Is the annotation to GO:0070587 too interpretive? Do later experiments provide more evidence for this interpretation?
Figure 2D Complete intercalation and a single row of dorsal epidermal cells are seen in the WT embryo, whereas cell migration is abnormal or blocked in ulp-2(RNAi) embryos (38 of 83 arrested embryos). ulp-2 dorsal intercalation defective (WBPhenotype:0001907) embryo Ce (WBls:0000003); abnormal (PATO:0000460),

hypodermis (WBbt:0005733); abnormal (PATO:0000460), embryo development (GO:0009790); abnormal (PATO:0000460), cell morphogenesis (GO:0000902); abnormal (PATO:0000460),

GO:0016331 morphogenesis of embryonic epithelium

GO:0010631 epithelial cell migration

Create a new GO BP term for dorsal intercalation?
Figure 2E In WT embryos, the lateral seam cells are cuboidal and arranged in a single row along the anterior-posterior axis. These cells play a key role in transmitting contractile forces to the dorsal and ventral cells during elongation. In ulp-2(RNAi) embryos, the cells are misshapen and mispositioned (29 of 83 arrested embryos). ulp-2 seam cell morphology variant ( WBPhenotype:0002176 ) embryo Ce (WBls:0000003); abnormal (PATO:0000460),

seam cell (WBbt:0005753) ; abnormal (PATO:0000460), cell morphogenesis (GO:0000902); abnormal (PATO:0000460)

GO:0016331 morphogenesis of embryonic epithelium Create a new GO BP term for embryonic elongation?
Figure 2F, S2E In the WT embryo at the end of ventral enclosure, opposing ventral epidermal cells form contacts at the ventral midline and establish new junctions. In the ulp-2(RNAi) class II embryo, the ventral cleft remains open (Figure S2), and the epidermal enclosure is physically blocked (26 of 81 arrested embryos). ulp-2 ventral closure defective (WBPhenotype:0001908) embryo development (GO:0009790); abnormal (PATO:0000460) GO:0016331 morphogenesis of embryonic epithelium Create new GO terms for ventral cleft closure (gastrulation cleft closure) and ventral epidermal enclosure?
Figure 3A-C,G,H, Table S1 Induction (by heat shock) of ULP-2(C743S) expression at the end of gastrulation prior to gastrulation cleft closure generated a robust and uniform phenotype characterized by epidermal enclosure failure (Figures 3A-3C, 3G, and 3H; Table S1; Movie S5). During normal development, ventral neuroblasts migrate to close the gastrulation cleft and form the substrate for subsequent migration of ventral epidermal cells (Chisholm and Hardin, 2005; Sulston et al., 1983). In ULP-2(C743S) embryos, the ventral cleft remained open, preventing epidermal enclosure and causing spillage of internal cells through the ventral surface of the epidermis. ulp-2 ventral closure defective (WBPhenotype:0001908) embryo Ce (WBls:0000003); abnormal (PATO:0000460),

embryo development (GO:0009790); abnormal (PATO:0000460), hypodermis (WBbt:0005733); abnormal (PATO:0000460), gastrulation (GO:0007369); abnormal (PATO:0000460)

GO:0016331 morphogenesis of embryonic epithelium Create new GO terms for ventral cleft closure (gastrulation cleft closure) and ventral epidermal enclosure?
Figure 3E; Movie S5 The epidermal enclosure arrest phenotype was also observed when ULP-2(C743S) was expressed under the control of the epithelial apical junction protein DLG-1 promoter (Figure 3E; Movie S5). Since DLG-1 is mainly expressed in epidermal cells from early epidermal morphogenesis, this observation supports the requirement for ULP-2 activity during epidermal morphogenesis. ulp-2 ventral closure defective (WBPhenotype:0001908) embryo Ce (WBls:0000003); abnormal (PATO:0000460),

embryo development (GO:0009790); abnormal (PATO:0000460), hypodermis (WBbt:0005733); abnormal (PATO:0000460)

GO:0016331 morphogenesis of embryonic epithelium Create new GO term for ventral epidermal enclosure?
Figure 5F To determine whether HMR-1 is sumoylated in vivo, authors immunoprecipitated extracts of HMR-1::GFP embryos with anti-GFP antibody followed by western blotting with anti-SUMO antibody (Figure 5F). Authors identified two slow-migrating forms of HMR-1::GFP on the anti-SUMO immunoblots (Figure 5F, lanes 2-4), and these were more abundant in HMR-1::GFP;ulp-2(RNAi) embryos, suggesting that ULP-2 regulates HMR-1 sumoylation in vivo (Figure 5F, lanes 3 and 4). ulp-2 protein sumoylation variant (WBPhenotype:0002362) embryo Ce (WBls:0000003); abnormal (PATO:0000460),

regulation of protein sumoylation (GO:0033233)

GO:0016926 protein desumoylation Rule of thumb for GO - is the gene product part of the process or does it regulate the process?
Figure 5F To determine whether HMR-1 is sumoylated in vivo, authors immunoprecipitated extracts of HMR-1::GFP embryos with anti-GFP antibody followed by western blotting with anti-SUMO antibody (Figure 5F). Sumoylated HMR-1 was undetectable in extracts of HMR-1::GFP embryos in which ULP-2 was overexpressed via a heat shock promoter (Figure 5F, lane 5, and Figure 5G). ulp-2 protein sumoylation variant (WBPhenotype:0002362) embryo Ce (WBls:0000003); abnormal (PATO:0000460),

regulation of protein sumoylation (GO:0033233)

GO:0016926 protein desumoylation
Figure 6A-C Overexpression of ULP-2, which prevents HMR-1 sumoylation (Figures 5F and 5G), showed HMR-1::GFP basolateral retention (Figures 6A-6C). ulp-2 protein subcellular localization variant (WBPhenotype:0000436) embryo Ce (WBls:0000003); abnormal (PATO:0000460),

apical protein localization (GO:0045176); abnormal (PATO:0000460)

GO:1904702 regulation of protein localization to cell-cell adherens junction New GO term requested for this paper.
Figures 6A-6C; Figures S3A and S3B HMR-1 localization was examined in embryos with hmp-2 RNAi-induced impairment of interactions between HMR-1 and F-actin. The embryos displayed aberrant basolateral accumulation of HMR-1::GFP, suggesting that mislocalization of sumoylated HMR-1 is the result of its dissociation from the actin cytoskeleton, which may affect both its apical recruitment and its stability at adherens junctions (AJ) (Figures 6A-6C; Figures S3A and S3B). hmp-2 protein subcellular localization variant (WBPhenotype:0000436) embryo Ce (WBls:0000003); abnormal (PATO:0000460),

apical protein localization (GO:0045176); abnormal (PATO:0000460)

I didn't make a GO annotation for hmp-2 here; will look again to see what might be applicable.
Figures 6A-6C In embryos carrying WT HMR-1::GFP, fluorescence at the apical adherens junction (AJ) increased linearly with time (Figures 6A-6C). In contrast, HMR-1::GFP was retained along the basolateral membrane in embryos subjected to ulp-2 RNAi; thus, localization of HMR-1 to AJs was abolished. ulp-2 protein subcellular localization variant (WBPhenotype:0000436) embryo Ce (WBls:0000003); abnormal (PATO:0000460),

apical protein localization (GO:0045176); abnormal (PATO:0000460)

GO:1904702 regulation of protein localization to cell-cell adherens junction New GO term requested for this paper.
Figure 6D DLG-1 localization was normal in ulp-2(RNAi) and hmp-2(RNAi) embryos. ulp-2, hmp-2 NOT transgene subcellular localization variant ( WBPhenotype:0000679 ) embryo Ce (WBls:0000003); abnormal (PATO:0000460),

protein localization (GO:0008104); abnormal (PATO:0000460)

Did not make any GO annotation here. How are NOT annotations handled with PATO-style phenotype annotations?
Figures 6B and 6D In contrast to loss of polarity and DLG-1 punctae appearance indicating fragmented junctions and abnormal apicobasal polarity that have been reported previously for let-413(RNAi) embryos (Legouis et al., 2000) (Figures 6B and 6D), DLG-1 localization was normal in ulp-2(RNAi) and hmp-2(RNAi) embryos. let-413 cell junction variant (WBPhenotype:0001657)

transgene subcellular localization variant (WBPhenotype:0000679)

embryo Ce (WBls:0000003); abnormal (PATO:0000460),

embryonic cell (WBbt:0007028); abnormal (PATO:0000460), protein localization (GO:0008104); abnormal (PATO:0000460), cell-cell contact zone (GO:0044291); abnormal (PATO:0000460)

GO:0045197 establishment or maintenance of epithelial cell apical/basal polarity

GO:0034332 adherens junction organization

Figure 7A,B The cadherin-catenin complex (CCC) is lost from the apical cell junctions upon muscle twitching in ulp-2(RNAi) embryos, whereas the DLG-1/AJM-1 complex (DAC) (DLG-1::RFP) is not affected. ulp-2 intercellular junction variant (WBPhenotype:0001658),

protein complex organization variant (WBPhenotype:0002132), transgene subcellular localization variant (WBPhenotype:0000679)

embryo Ce (WBls:0000003); abnormal (PATO:0000460),

catenin complex (GO:0016342); mislocalised (PATO:0000628)

GO:0034334 adherens junction maintenance

happens_during (GO:0071260) response to mechanical stress happens_during (GO:0016331) morphogenesis of embryonic epithelium

Figure 7C-E Embryos subjected to ulp-2 RNAi exhibited discontinuous HMR-1::GFP foci and collapsed actin bundles (Figures 7C-7E). In WT embryos, actin bundles are arranged in parallel bands, and HMR-1::GFP is localized at the base of the actin bundle anchoring it to the membrane at AJs. In ulp-2(RNAi) embryos, loss of HMR-1 at the apical junction is accompanied by collapse and random spacing of actin bundles. ulp-2 transgene subcellular localization variant (WBPhenotype:0000679),

circumferential actin bundles disorganized (WBPhenotype:0002124)

embryo Ce (WBls:0000003); abnormal (PATO:0000460),

actin filament bundle assembly (GO:0051017)

GO:0034334 adherens junction maintenance

happens_during (GO:0071260) response to mechanical stress happens_during (GO:0016331) morphogenesis of embryonic epithelium



Existing GO Terms

GO:0007369 gastrulation

GO:0003381 epithelial cell morphogenesis involved in gastrulation

GO:0070587 regulation of cell-cell adhesion involved in gastrulation

GO:0016331 morphogenesis of embryonic epithelium

GO:0010172 embryonic body morphogenesis

GO:1904696 protein localization to cell-cell adherens junctions

GO:1904704 positive regulation of protein localization to cell-cell adherens junctions

GO:0016926 protein desumoylation

GO:0034334 adherens junction maintenance

GO:0071260 cellular response to mechanical stimulus


Possible New GO Terms

GO:new? ventral cleft closure?

GO:new? ventral epidermal enclosure?

GO:new? dorsal intercalation?

GO:new? embryonic elongation?

GO:new? regulation of cell-cell adhesion involved in morphogenesis of embryonic epithelium?

GO:new? positive regulation of protein localization to cell-cell adherens junctions via protein desumoylation?


Chris' allele-phenotype EQ-PATO annotations

anatomical structure morphogenesis (Figure 4A)

apical protein localization (Figure 6A-C)

developmental process (Figure 4B)

embryo development (Figure S2A,D, 3E, 4A)

embryo development, gastrulation (Figures 3A-3C, 3G, and 3H; Table S1; Movie S5)

gastrulation PATO: failure/non-functional (Figure S2A,D, 4A)

regulation of protein sumoylation (Figure 5F)


Chris' RNAi EQ-PATO annotations:

actin filament bundle assembly (Figure 7C-E)

apical protein localization (Figure 6)

body morphogenesis (Figure 4B, Movie S6)

cell morphogenesis (Figure 2E)

embryo development (Figure 2C,D,F, 4A, S2A,D)

digestive tract development (Figure S2F)

gastrulation (Figure 2C,S2D,F, 4A,B, Movie S6)

neuroblast migration (Figure S2E)

protein localization (Figure 6D)

regulation of protein sumoylation (Figure 5F)

catenin complex PATO: mislocalized (Figure 7A,B)

cell-cell contact zone (Figure 6D, S3D,E)