Biology:Trans-Golgi network vesicle protein 23 A

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Short description: Mammalian protein found in Homo sapiens

Trans-Golgi network vesicle protein 23 A (TVP23A) is a protein coded for the TVP23A gene, formerly known as FAM18A.[1] TVP23A is located on chromosome 16.[2] It is known to have human paralogs, TVP23B and TVP23C, as well as orthologs in many different species, notably yeast, mice, and chickens.[3] The general consensus on the TVP23A protein indicate that it has some function in the late Golgi apparatus and is involved in retrograde transport from endosomes back into the Golgi apparatus. The nature of this transport is still unknown.[4]

Gene

Locus

TVP23A is located at cytogenic band 16p13.13, on the negative strand of Chromosome 16.[2]

Location of TVP23A on Chromosome 16 (red line)

Alternative Names

TVP23A stands for Trans-Golgi network Vesicle Protein 23A TVP23A, is the current name for the protein. Aliases of TVP23A include FAM18A, and rarely YDR084C.[1]

mRNA

Isoforms

There are two known isoforms of TVP23A, variant one and variant two, with variant one being the more common variant in humans.[2]

Protein

Structure

TVP23A is a member of the pfam superfamily containing the domain of unknown function 846 (DUF846).[5] TVP23A has a predicted molecular weight of 24.1 kilodaltons, an isoelectric point of 6.5, and relatively high amounts of tryptophan and phenylalanine.[6] The secondary structure of TVP23A consists primarily of alpha helices composing 4 transmembrane domains.[7] There is not much information on the tertiary structure of TVP23A or its homologs. iTASSER[8] was used to generate a prediction for the folding pattern of TVP23A, which supports the presence of multiple helix structures.

Protein structure of TVP23A as predicted by iTASSER

Expression

TVP23A is ubiquitously expressed in all human tissues.[9] There is evidence of higher expression in the brain tissue of mice.[10] The promoter for TVP23A is GXP_91266, spanning 1403 base pairs located on the negative strand of chromosome 16.[11]

Function

The hypothesized function of TVP23A is a transmembrane protein involved in retrograde transport of vesicles from early endosomes into the late Golgi apparatus.[12] TVP23A interactions with SNARE TVI1 were found to be required for retrograde transport. [13]

Interacting Proteins

TVP23A has been found to interact with four different proteins via Yeast two hybrid arrays.[14] Two of these proteins, YIPF1 and YIPF2, are believed to be Golgi transport proteins.

Protein Experiment Function
SCAND1 Two hybrid array Potentially a transcription factor (SCAN domains common in ZFP)
WIPF2 Two hybrid array Believed to be involved in actin filament remodeling
YIPF1 Two hybrid array Golgi transport protein
YIPF2 Two hybrid array Golgi transport protein

Homology

Homologous Domains

TVP23A is a DUF846 containing protein, which is homologous throughout TVP-type proteins. This domain contains the 4 transmembrane domains of TVP23A[15]

Paralogs

TVP23A has two paralogs, TVP23B and TVP23C. TVP23B and TVP23C are 96% similar to each other, and both are located on chromosome 17.[16] Due to the locations of these three genes, and their identities to each other, it is probable that ancestral TVP23 underwent duplication and translocation, giving rise to TVP23A on chromosome 16 and TVP23B/C on chromosome 17, which then underwent a second duplication to form TVP23B and TVP23C.

Gene Seq Length Seq Identity Chromosome
TVP23A 213 100% 16
TVP23B 205 54% 17
TVP23C 203 53% 17

Orthologs

TVP23A has been found in all multicellular eukaryotes, including fungi. This gene has not been found in bacteria.[17]

Genus and species Common Name Order Date of Divergence NCBI Accession Number Seq Length Seq Identity
Homo sapiens Human Primate 0 NP_001072980 213 100%
Pan troglodytes Chimp Primate 6.4 XP_009428557.1 213 98%
Mus musculus Mouse Rodentia 88 NP_001013800.1 222 85%
Rattus norvegicus Rat Rodentia 88 NP_001101733.1 222 84%
Canis lupus familiaris Dog Carnivora 94 XP_547129.2 213 97%
Camelus ferus Wild Bactian Camel Ceratiodactyla 94 XP_006190640.1 213 92%
Bubalus bubalis Water Buffalo Ceratiodactyla 94 XP_006068214.1 213 93%
Miniopterus natalensis Natal Long-fingered Bat Chiroptera 96 XP_016053077.1 213 93%
Myotis brandtii Brandt's Bat Chiroptera 96 XP_005871809.1 213 93%
Condylura cristata Star Nose Mole Soricomorpha 96 XP_012587517.1 213 92%
Erinaceus Europaeus European Hedgehog Soricomorpha 96 XP_016047734.1 251 68%
Falco peregrinus Peregrin Falcon Aves 312 XP_005244242.1 204 64%
Gallus gallus Chicken Aves 320 XP_015150063.1 213 74%
Gekko japonicus Schlegel's Japanese Gecko Reptile 320 XP_015265390.1 210 75%
Thamnophis sirtalis Garter Snake Reptile 320 XP_013925075.1 308 30%
Rana catesbeiana American Bullfrog Amphibian 352 ACO51802.1 206 52%
Xenupus tropicalis African Clawed Frog Amphibian 353 XP_017953113.1 198 71%
Callorhinchus milii Australian Ghostshark Chimaeriformes 465 XP_007903081.1 206 70%
Rhizopus microsporus Rhizopus Fungi 1105 CEI91429.1 231 35%
Mortierella elongata Mortierella Fungi 1105 OAQ36303.1 218 35%
dictyostelium lacteum Dictyostelium Fungi 1480 KYQ94004.1 220 34%

References

  1. ↑ 1.0 1.1 "TVP23A". https://www.ncbi.nlm.nih.gov/gene/780776. 
  2. ↑ 2.0 2.1 2.2 "GeneCards". https://www.genecards.org/cgi-bin/carddisp.pl?gene=TVP23A. 
  3. ↑ "AceView". https://www.ncbi.nlm.nih.gov/ieb/research/acembly/av.cgi?db=human&c=Gene&l=FAM18A. 
  4. ↑ "GenAtlas". http://genatlas.medecine.univ-paris5.fr/fiche.php?n=28506. 
  5. ↑ "DUF846". https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=191380. 
  6. ↑ "SAPS". SDSC. http://seqtool.sdsc.edu/CGI/BW.cgi#!. [no|permanent dead link|dead link}}]
  7. ↑ "TMHMM". http://seqtool.sdsc.edu/CGI/BW.cgi#!. [no|permanent dead link|dead link}}]
  8. ↑ "I-TASSER server for protein structure and function prediction". http://zhanglab.ccmb.med.umich.edu/I-TASSER/. 
  9. ↑ "Gene: TVP23A" (in en-gb). http://www.ensembl.org/Homo_sapiens/Gene/ExpressionAtlas?g=ENSG00000166676;r=16:10760919-10818794. 
  10. ↑ "GDS3142 / 1435130_at". https://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS3142:1435130_at. 
  11. ↑ "ElDorado". https://www.genomatix.de/. 
  12. ↑ Inadome, Hironori; Noda, Yoichi; Kamimura, Yurika; Adachi, Hiroyuki; Yoda, Koji (February 2007). "Tvp38, Tvp23, Tvp18 and Tvp15: Novel membrane proteins in the Tlg2-containing Golgi/endosome compartments of Saccharomyces cerevisiae". Experimental Cell Research 313 (4): 688–697. doi:10.1016/j.yexcr.2006.11.008. PMID 17178117. 
  13. ↑ Stein, Ivar S.; Gottfried, Anna; Zimmermann, Jana; Fischer von Mollard, Gabriele (1 April 2009). "interacts genetically with the yeast SNARE and functions in retrograde transport from the early endosome to the late Golgi". Biochemical Journal 419 (1): 229–236. doi:10.1042/BJ20081973. PMID 19076069. https://hal.science/hal-00479102/file/PEER_stage2_10.1042%252FBJ20081973.pdf. 
  14. ↑ "IntAct" (in en). http://www.ebi.ac.uk/intact/. 
  15. ↑ "Pfam: Family: DUF846 (PF05832)". http://pfam.xfam.org/family/PF05832. 
  16. ↑ "BLAST: Basic Local Alignment Search Tool". https://blast.ncbi.nlm.nih.gov/Blast.cgi. 
  17. ↑ "UCSC Genome Browser Home". https://genome.ucsc.edu/. 



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