XB-FEAT-29081014

nomenclature changes

05MAR2024

Following analysis below (synteny and protein domain) and after comparing nomenclature for PX domain-containing proteins in other taxa, Xenbase suggested names are as follows snx34, PXA and sorting NEXIN domain contain protein

synteny

Human. X: SLC25A43> SLC25A5> STEEP1< UBE2A> NKRF< SEPTIN6<

Xtrop chr8: slc25a43> slc25a5> LOC100492077> ube2a> nkrt< nkap>

Xla v10 8L: slc25a43.L> slc25a5.L> ... ube2a.L> nkrf.L< septin6.L<

Xla v10 chr8S: LOC# slc25a5.S> LOC108700137> ube2a.S>. nkrf.S<

Notes from synteny:

• • the gene is NOT PRESENT IN XLA.L sub genome, although LOC108700137 and LOC100492077 both appear to be good protein coding Xenopus paralogs.

• • Conserved synteny with human identifies STEEP1, STING1 ER exit protein 1 as potential ID and ortholog.

• • However, InterPro does not find any domain in common between Hsa.STEEP1 versus LOC108700137 and LOC100492077.

• • STEEP1 is a short 173 AA protein. The 2 Xenopus loci are much larger, with 605 (Xtr) and 700 (Xla.S) AAs respectively.

• • For Xtrop protein: InterPro Protein family membership: None predicted

protein characterization

05MARCH2024

Hsa.STEEP1 NP_001164040.1 >NP_001164040.1 STING ER exit protein isoform 2 [Homo sapiens] MRPRDRSRVIDAAKHAHKFCNTEDEETMYLRRPEGIERQYRKKCAKCGLPLFYQSQPKNAPVTFIVDGAV VKFGQGFGKTNIYTQKQEPPKKVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQL ERKGMSKRRLQELAELEAKKAKMKGTLIDNQFK

InterPro domain search shows this 173AA protein "includes protein STEEP (CXorf56) from humans and related proteins. STEEP interacts with STING and enables STING signaling by promoting ER exit"

NB: no domains uncommon with the Xenopus proteins, details below.

The X. tropicalis ad the X. laevis protein both contains a PXA domain and a sorting NEXIN domain.

InterePro entry for PXA/ Phox associated  domains:

The PX-associated (PXA) domain is a ~200-amino acid module of unknown function. Perhaps it is required for protein-protein interaction and/or filament formation. In addition to the phosphoinositide-binding PX domain, the PXA domain can also be associated with a transmembrane domain and RGS, which binds to activated G- alpha subunits and is responsible for GTPase activating protein (GAP) function [2][1]. Some proteins known to contain a PXA domain are listed below: - Mammalian sorting nexins (SNXs) 13, 14 and 19. - Yeast structural protein MDM1. The profile we developed covers the entire PXA domain.

InterPro entry for  sorting NEXIN domains:

The protein family in question belongs to the sorting nexin family, which plays a crucial role in intracellular trafficking. These proteins are involved in several stages of intracellular trafficking, including endosome-to-Golgi protein transport, vesicle trafficking, and exocytosis. Some members of this family are essential for mitotic growth and organelle inheritance. They also contribute to maintaining normal neuronal excitability and synaptic transmission. Certain proteins in this family are required for autophagosome clearance, possibly by mediating the fusion of lysosomes with autophagosomes. They interact with membranes containing phosphatidylinositol 3-phosphate and bind phosphatidylinositol 3,5-bisphosphate, a key component of late endosomes/lysosomes. Some proteins in this family may also play a role in insulin secretion and in maintaining insulin-containing dense core vesicles in pancreatic beta-cells. Additionally, some members of this family are involved in vacuolar morphogenesis and meiosis.