Table 1.
Cell-type specific expression of epithelial cell markers in Hydra (for protein sequences and expression levels see Supplemental Data). Table showing the relative level of expression of several classes of epithelial markers in the ectodermal epithelial cells (ecto), endodermal epithelial cells (endo) or interstitial cells (i-cells) of the body column of AEP Hydra as deduced from quantitative RNA-seq applied to GFP-sorted cells (see Fig. 2A). “Expressing cells” column: >>> or <<< indicate a minimal 10× difference, >> or << a minimal 2× difference, uppercase writing indicates over 1'000 reads. Hydra protein sequences are available on Uniprot.org either as individual sequences or as sequences from RNA-seq transcriptomes designed to identify cell-type specific proteins,10 Hydra vulgaris/human orthologs,91,92 GO-annotated immune proteins,82 neuromuscular transmission proteins,14 epithelial markers (this work, all annotated protein sequences are accessible from UniProt release 2015_10. For the nomenclature of claudin-like proteins, see Ganot et al. 2015 (ref. 21).)
| Predicted FUNCTIONS | PROTEIN NAMES Gene families | EXPRESSION in GFP Hv-AEP CELLS | Protein ACCESSION (Hv-Basel, Zürich, Jussy) |
|---|---|---|---|
| Sub-apical complex | INADL InaD-like protein (PatJ) | ECTO > Endo >> i-cells | T2M9I3_HYDVU |
| LIN7C Protein lin-7 homolog C | Ecto, Endo > i-cells | T2M567_HYDVU | |
| MPP5 MAGUK p55 (Stardust, Pals1) | Ecto > Endo >> i-cells | T2M9J3_HYDVU | |
| Notch2 (Crumbs-like) | ENDO >>> Endo >> i-cells | T2MDK9_HYDVU | |
| Apico-lateral complex | CDC42 Cell division control protein 42 homolog | ENDO > ECTO > I-CELLS | T2MEG1_HYDVU |
| PARD3 Partitioning defective 3 homolog | ECTO > ENDO > i-cells | T2M994_HYDVU | |
| PARD6G Partitioning defective 6 homolog gamma | Ecto > Endo >> i-cells | T2M6J3_HYDVU | |
| PRKCI Protein kinase C | ECTO > Endo >> i-cells | T2MGA0_HYDVU | |
| Lateral complex | DLG1 Disks large homolog 1 | ECTO > ENDO >> I-CELLS | T2ME64_HYDVU |
| DLG5 Disks large homolog 5 | Ecto >> Endo, i-cells | T2M8B5_HYDVU | |
| LLGL1 Lethal(2) giant larvae prot. homolog 1 | ECTO > ENDO > I-CELLS | T2MCV2_HYDVU | |
| SCRIB Protein scribble homolog | ECTO > ENDO > I-CELLS | T2MDC2_HYDVU | |
| Structural | CLDN-l1, 7, 12 Claudin-like 1,7, 12 | ECTO > ENDO >> i-cells | CRX73236, CRX73250, CRX73241 |
| Septate Junctions | CLDN-l10 Claudin-like 10 | ECTO >> Endo >> i-cells | CRX73238, |
| (St SJs) | CLDN-l2, 9, 11 Claudin-like 2,9,11 | Ecto << Endo >> i-cells | CRX73242, CRX73253, CRX73239 |
| CLDN-l3, CLDN-l4, Claudin-like 3, 4 | Ecto, Endo | CRX73247, T2MFM9_HYDVU | |
| CLDN-l5 Claudin-like 5 | Ecto > Endo >> i-cells | T2MBI9_HDYVU | |
| CLDN-l6, 8, 14, 15 Claudin-like 6,8,14,15 | No or very low expression | CRX73249, CRX73252, CRX73244, CRX73246 | |
| CNTN2 Contactin 2 | ENDO > ECTO >> i-cells | T2MEK3_HYDVU | |
| CNTN4 Contactin 4 | ECTO >> ENDO >> i-cells | CRX73254 | |
| CNTNAP2 Contactin assoc. prot 2 | ECTO > ENDO >> i-cells | T2M432_HYDVU | |
| CNTNAP2l Contactin assoc. prot 2like | Ecto > i-cells > Endo | CRX73256 | |
| CNTNAP4 Contactin assoc. prot 4 | Ecto >> Endo | CRX73257 | |
| CNTNAP4l Contactin assoc. prot 4like | Ecto, Endo << I-CELLS | CRX73258 | |
| CNTNAP5 Contactin assoc. prot.-like 5 | ECTO > ENDO >> i-cells | T2M8X1_HYDVU | |
| CNTNAP53l Contactin assoc. prot. like 5-3 | Ecto >> endo | CRX73259 | |
| DSCAM Down syndrome cell adhesion mol. | Endo < Ecto < i-cells | T2MIF2_HYDVU | |
| NRXN1 Neurexin-1a like | Apical expression only | CRX73281 | |
| NRXN3 Neurexin-3a like | ECTO >> Endo > i-cells | T2M365_HYDVU | |
| Scaffold | ATP1A1 NaK ATPase-α1 | ECTO >>> Endo, i-cells | CRX73229 |
| Septate Junctions | ATP1A2 NaK ATPase-α2 | ECTO >> Endo >> i-cells | CRX73230 |
| (Sc SJs) | ATP1A3 / AT1A NaK ATPase-α3 | ECTO < ENDO < I-CELLS | AT1A_HYDVU, T2MGY6_HYDVU |
| ATP1A4 NaK ATPase-α4 | Ecto | CRX73232 | |
| ATP1A5 NaK ATPase-α5 | Ecto > Endo > i-cells | CRX73233 | |
| ATP1B1 NaK ATPase-β2 (NRV Nervana) | ECTO > I-CELLS > ENDO | T2MHY2_HYDVU | |
| EPB41L4A Band 4.1 l4 (Coracle) | Endo > Ecto > i-cells | T2M572_HYDVU | |
| EPB41L5 Band 4.1 l5 (Yurt) | ECTO >> Endo >> i-cells | T2M5L9_HYDVU | |
| ZO-1 Zonula Occludens 1 (TJP1) | ECTO >> ENDO >> i-cells | T2MDH6_HYDVU | |
| Adherens Junctions | ACTN1 α-actinin | ECTO > ENDO >> i-cells | T2MHI5_HYDVU |
| (AJs) | CDH Classical cadherin | ECTO >> i-cells >> Endo | CRX73223 |
| CELSR2 Cadherin EGF LAG 7pass | ECTO > Endo > i-cells | T2M506_HYDVU | |
| CTNNA1 α-catenin | ECTO >> i-cells, Endo | T2M3Z5_HYDVU | |
| CTNNB1 β-catenin | ENDO > I-CELLS> ECTO, | T2MGP6_HYDVU | |
| CTNND2 δ-catenin | Ecto > i-cells > Endo | T2M3M0_HYDVU | |
| DAG1 Dystroglycan | Ecto | T2MDZ1_HYDVU | |
| DCHS1 Protocadherin 16 | Ecto > Endo> i-cells | T2M7D2_HYDVU | |
| FAT1 Protocadherin 1 | ENDO > ECTO >> i-cells | T2MDR8_HYDVU | |
| FAT4l Protocadherin Fat4-like | ENDO >> ECTO > i-cells | CRX73260 | |
| MICALl2 MICAL like protein 2 | ECTO > Endo > i-cells | T2MAH1_HYDVU | |
| MLLT4 (Afadin) | ECTO >> ENDO >> i-cells | T2MF28_HYDVU | |
| SGCE Sarcoglycan | Endo > Ecto > i-cells | T2MJ55_HYDVU | |
| VCL Vinculin | ECTO > ENDO >> I-CELLS | T2MH95_HYDVU | |
| Gap junctions (GJs) | Inx1, Innexin 1 | ENDO > ECTO >>> i-cells | Q2EMV6_HYDVU, |
| Inx2, Inx9, Inx10, Inx11, Inx14, Inx15 | No or very low expression in body column | seq57378, seq46622 (pending), CRX73266, seq79106, seq05316, seq64623 (pending) | |
| Inx3, Inx13 Innexin 3, 13 | ECTO > ENDO >> i-cells | CRX73271, CRX73269 | |
| Inx4, Inx5, Inx6, Inx7, | ECTO or Ecto | CRX73272, CRX73275, CRX73274, CRX73277, | |
| Inx8 Innexin 8 | I-CELLS >> Ecto >> Endo | Seq55322 (pending) | |
| Inx12 Innexin12 | Endo >> Ecto >>> i-cells | CRX73268 | |
| Hemi-desmosomes | ADAM10 | ECTO > ENDO >> i-cells | T2MJ41_HYDVU |
| (HDs) | ADAM12 | Endo > Ecto > i-cells | T2MIA5_HYDVU |
| ADAM17 | ECTO < ENDO < I-CELLS | T2MEE2_HYDVU | |
| ADAM33 | Ecto < Endo < i-cells | T2M6H9_HYDVU | |
| ADAMTS9 Disintegrin MP thrombospondin | Endo > i-cells > Ecto | T2M4C5_HYDVU | |
| CIB1 Calcium and integrin-binding protein 1 | Endo > Ecto >> i-cells | T2M774_Hydvu | |
| FAK1 Focal adhesion kinase | ECTO, ENDO >> i-cells | T2MDJ8_HYDVU | |
| ILK Integrin linked kinase | ECTO, ENDO >> i-cells | T2ME09_HYDVU | |
| ILKAP ILK-associated protein | ECTO < ENDO < I-CELLS | T2M6A7_HYDVU | |
| ITFG2 Integrin-a FG-GAP | Endo, i-cells > Ecto | T2M8F8_HYDVU | |
| ITGA4 integrin-alpha4 | ECTO > ENDO >> i-cells | CRX73278 | |
| ITGA8 Integrin-alpha8 | ENDO > ECTO > I-CELLS | T2MFQ0_HYDVU | |
| ITGA9 Integrin-alpha9 | ECTO > ENDO >>i-cells | T2ME15_HYDVU | |
| ITGB1 Integrin-beta1 | ECTO >> ENDO >> i-cells | T2MHW4_HYDVU | |
| ITGB2 Integrin-beta2 | ECTO > ENDO >> I-CELLS | T2MGW7_HYDVU | |
| ITGB3 Integrin-beta3 | Ecto >>> Endo < i-cells | CRX73280 | |
| PXN Paxillin | ENDO > ECTO >> I-CELLS | T2MG05_HYDVU | |
| TLN2 Talin2 | ECTO > ENDO > I-CELLS | T2M2W2_HYDVU | |
| TNS1 Tensin1 | ECTO > Endo >>> i-cells | T2M5L6_HYDVU | |
| Cell adhesion | ANX12 Annexin XII / Annexin –B12 | ENDO > ECTO >>> i-cells | P26256_HYDVU |
| Scaffolding proteins | ANXA7 Annexin | ECTO > ENDO >> i-cells | T2MGP1_HYDVU |
| CASK Peripheral plasma mbne protein CASK | Ecto >> Endo, i-cells | CRX73235 | |
| DSCAM Down syndrome cell adhesion mol | Endo < Ecto < i-cells | T2MIF2_HYDVU | |
| EpH1 Ephrin receptor 1 | ENDO >>> i-cells, Ecto | AGO06063.1 | |
| EpH2 / EPHA7 Ephrin receptor 2/7 | ECTO, Endo >> i-cells | AGO06064.1, T2MDF6_HYDVU | |
| EpH3 / EPHA5 Ephrin receptor 3/5 | ECTO >>> i-cells, endo | AGO06066.1, T2MF36_HYDVU | |
| EpH4 / EPHA4 Ephrin receptor 4 | Endo >> Ecto > i-cells | AGO06065.1, T2MEM7_HYDVU | |
| EpHB1 Ephrin ligand B1 | Ecto >>> i-cells, Endo | AGO06067.1, R9WY58_HYDVU | |
| EpHB2 Ephrin ligand B2 | Ecto, Endo << i-cells | AGO06068.1, R9WWC9_HYDVU | |
| EpHB3 Ephrin ligand B3 | ENDO >> Ecto >> i-cells | AGO06069.1, R9X0X4_HYDVU | |
| FARP2 l FERM RhoGEF pleckstrin domain | Ecto > Endo >> i-cells | T2MID3_HYDVU | |
| GUK1 like Guanylate Kinase 1 | Ecto, Endo > i-cells | T2MD66_HYDVU | |
| IQGAP / IQGAP1 GTPase-activating like prot | ENDO > ECTO > I-CELLS | Q9XZE9_HYDVU, T2MFN7_HYDVU | |
| LRIG3 Leu Rich Repeats Ig-like prot 3 | Ecto > Endo > i-cells | T2MAL0_HYDVU | |
| Trop1 Tropomyosin | ECTO >>> Endo | TPM1_HYDVU | |
| Cuticle structure | Sweet Tooth proteins | 22 proteins | See Böttger et al. 2012 (ref. 16) |
| PPOD1 Putative Peroxidase 1 | ECTO >> ENDO >>> i-cells | Q2FBK4_HYDVU, Q2FBK7_HYDVU | |
| PPOD2 Putative Peroxidase 2 | No PPOD2 in Hv-AEP | Q962G1_HYDVU, Q2FBK2_HYDVU | |
| PPOD2-like Putative Peroxidase 2-like | No PPOD2l in Hv-AEP | Q2FBJ9_HYDVU | |
| Extra-Cellular Matrix | ANKFN1 Ankyrin repeat fibronectin III | Ecto > Endo >> i-cells | T2M9C4_HYDVU |
| (ECM) | COL4A1 / COL4A5 collagen-alpha5 (IV) | ENDO >>> Endo, i-cells | Q9GQB1, T2MFW7_HYDVU |
| FARM1 secreted astacin | Endo >>> Ecto | Q9U4X9_HYDVU | |
| FiCol fibrillar collagen | ENDO >>>> Ecto, i-cells | Q8MUF5_HYDVU | |
| FNDC3B FN type III containing protein 3A | ECTO, ENDO >> i-cells | T2MCC9_HYDVU | |
| HMCN1l1 Hemicentin1 like1 | ENDO >>> i-cells > Ecto | CRX73261 | |
| HMCN1l2 Hemicentin1 like2 | ENDO >> i-cells > Ecto | CRX73263 | |
| HMCN2l1 Hemicentin2 like1 | ECTO >>> i-cells, Endo | CRX73264 | |
| HMP1 Metalloendopeptidase | ENDO >> Ecto > i-cells | Q25174_HYDVU | |
| HSPG2 basement membrane-specific heparan sulfate proteoglycan protein | ENDO >> i-cells > Ecto | T2MDT4_HYDVU | |
| LAMA5 Laminin subunit alpha-5 | ENDO >> Ecto > i-cells | T2MIW4_HYDVU | |
| LAMB1 Laminin subunit beta-1 | ENDO >>> i-cells > Ecto | LAMB1_HYDVU | |
| MMP matrix metalloproteinase | ENDO >>>> Ecto > i-cells | Q9U9P0_HYDVU | |
| MP2 Metalloendopeptidase (meprin-like) | Endo >> i-cells > Ecto | Q9XZG0_HYDVU | |
| Stem Cell Behavior | Ets1 / ERG | ECTO > ENDO >>> i-cells | I3V7X0_HYDVU, T2MHK5_HYDVU |
| & Stemness | Ets2 / GABPA | Endo > Ecto >> i-cells | T2MDI3_HYDVU |
| FoxO | ECTO > I-CELLS > ENDO | J7HWF0_HYDVU | |
| Klf1 Krueppel like factor 1 | ECTO > ENDO >>> i-cells | T2MDQ7_Hydvu | |
| Klf3 Krueppel like factor 3 | ECTO > Endo | I3V7X3_HYDVU | |
| Klf7 Krueppel like factor 7 | ECTO > ENDO >> i-cells | T2MIK5_Hydvu | |
| Klf8 Krueppel like factor 8 | ECTO > ENDO | I3V7V7_HYDVU | |
| Klf11 Krueppel like factor 11 | ECTO > ENDO >> i-cells | I3V7X4_HYDVU, T2MJ10_HYDVU | |
| Klf13 Krueppel like factor 13 | Endo < Ecto << I-CELLS | I3V7W6_HYDVU, T2M360_HYDVU | |
| MAX | ECTO < ENDO < I-CELLS | D0EM50_HYDVU | |
| Myc-1 | Endo < Ecto << i-cells | D0EM49_HYDVU | |
| Myc-2 | Ecto < ENDO < I-CELLS | D2KBP8_HYDVU, T2MH01_HYDVU | |
| Myc-3 | Endo < Ecto <<< i-cells | CRX73227 | |
| PIWIL1 /Hywi /Cniwi Piwi-like protein 1 | ENDO < ECTO < I-CELLS | T2M7W7, J7HWM3, T2HRA5 | |
| PIWIL2 / Hyli Piwi-like protein 2 | ENDO < ECTO << I-CELLS | T2M9F7, U5XHW4, T2HRQ9 | |
| PL10 | ENDO < ECTO < I-CELLS | Q9GV14_HYDVU | |
| POU4F2 | Endo << Ecto < i-cells | T2MDR7_HYDVU | |
| SOX2 | ECTO > Endo, i-cells | T2MFM3_HYDVU | |
| TCF Ternary Complex Factor | ENDO > I-CELLS > ECTO | Q9GTK1_HYDVU | |
| TCTP (p23) | ENDO > ECTO > I-CELLS | TCTP_HYDVU | |
| TP53BP2 | ECTO >> ENDO > i-cells | T2MDM1_HYDVU | |
| TP73 | Endo >> Ecto > i-cells | T2MIU9_HYDVU | |
| Vasa1 / Cnvas1 | ECTO < ENDO < I-CELLS | Q9GV13_HYDVU | |
| Vasa2 / Cnvas2 | ECTO < ENDO < I-CELLS | Q9GV12_HYDVU |