TMEM33

Transmembrane protein 33 is a protein that in humans, is encoded by the TMEM33 gene, also known as SHINC3. [1] Another name for the TMEM33 protein is DB83.

Gene

In humans, this gene’s DNA location is the short arm of chromosome 4, loci position: 4p13. [3] The genomic range is 41937502-41956213, spanning 18.7 kb, on the positive strand. [3] Transmembrane protein 33 is ubiquitously expressed, but is particularly highly expressed in the blood, lymph nodes, bone, and adipose tissue.[4] [5]

Promoter

Transcription factors with the highest matrix binding affinity to GXP_4428588[6]

A promoter sequence upstream of TMEM33 is GXP_4428588. This 1069 base pair promoter sequence spans 41936535-41937603 on human chromosome 4. [6] The promoter sequence overlaps with the 5' untranslated region, first coding exon, and first intron of the TMEM33 gene. Many different transcription factors are known to bind to this region. [6] The most likely to bind transcription factors are expressed most in connective tissue (i.e. blood, adipose tissue, and bone), the immune system, and nervous system. [6]

mRNA

All eleven human transcripts of TMEM33 aligned. The transcripts a, b, c, d, and e encode viable TMEM33 isoforms and the other six do not.[7]

Eleven different mRNA transcript variants of TMEM33 exist, 9 alternatively spliced variants and 2 unspliced forms.[7] Only 5 variants (a, b, c, d, and e) encode proteins. Transcripts a, b, and c encode the same 247 amino acid long protein because each have the same 7 typical coding exons. These three variants only vary in 3' UTR length. [7] Transcripts a, b, and c have a 744 base pair long coding range and a particularly long 3’ UTR that is 6000 base pairs long. [8]

Protein

Characteristics

SUSIO prediction of TMEM33 amino acid arrangement in human cellular membrane [9]

In Homo sapiens, TMEM33 protein has 5 different coding mRNA variants that encode 3 different protein isoforms.[10] The largest and most common human TMEM33 protein is 247 amino acid long protein with 3 transmembrane domains. [11] The only known TMEM33 ortholog with four transmembrane domains is Tts1 in Schizosaccharomyces pombe. [12] The human protein has a predicted molecular weight of 28 kDa [13] and an isoelectric point of 9.88. [14] TMEM33 has a significantly high net positive charge and quantity of hydrophobic residues. In particular, leucine that makes up 17.8% of the human TMEM33 protein. [14] TMEM33 contains a conserved domain in the protein super family UPF0121, in Homo sapiens this region spans from amino acids 1 to 246. [11]

Post-translation modifications

Programs and experiments that analyze proteins predict various post-translational modifications of TMEM33. There is an experimentally determined acetylation point is at alanine, amino acid residue 2 in humans. [11] Human TMEM33 has phosphorylation predicted on serine residues 197 and 198 and threonine residues 5, 127, and 193. [15] The primary kinases that are predicted to act on TMEM33 are Protein kinase C (PKC) and PKA. [16] TMEM33 is predicted to have an O-glycosylation site at human amino acid residues 4 and 5 [17]

Structure

The exact secondary structure of TMEM33 is unknown, but it is predicted to be composed primarily of alpha-helices and coiled domains. [14] The tertiary structure is unknown.

Cellular localization

According to the sequence motifs of the Homo Sapiens, TMEM33 it is predicted to be at the endoplasmic reticulum (ER) 48%, mitochondria 35%, and nucleus 13%. [12] TMEM33 orthologs in vertebrates, invertebrates, and fungi were also predicted to localize to these three cellular locations: the ER first and the mitochondria second, and some orthologs a third location was predicted and it was the nucleus. [12] Homo Sapiens TMEM33 localized with ER membrane and NE exogenously. [18] The fission yeast TMEM33 ortholog, Tts1, was reported to localize to the ER and to the NE (nuclear envelope). [19]

Homology

Orthologs of TMEM33 and their divergence from human TMEM33 as obtained from NCBI

A TMEM33 ortholog is known to be in over 150 organisms and no known paralogs exist. [1] TMEM33 is conserved throughout all animals, similarity to human TMEM33 is >80% for all vertebrates and >60% for all invertebrates. [20] TMEM33 has very distant orthologs that have UPF0121 in fungus, yeast, and plants. [20]

Protein Interactions

Using human proteins, an affinity chromatography ran on TMEM33 showed that the protein bound to reticulon 4C, 1A, 2B, 3C, and Arl6IP1 in vitro. [18] TMEM33 was found to interact with ubiquitin C, ubiquitin specific peptidase 19 (USP19), 40S ribosomal protein S14 (RPS14), replication protein A (RPA1, RPA2, RPA3), transitional endoplasmic reticulum ATPase (VCP), and RNA polymerase III initiation factor (BRF2) using affinity capture experiments with those proteins as bait. [21] Coimmunoprecipitation ecperiment found two-pore channel (TPC), an ion channel, and TMEM33 bind. [22]

Function

TMEM33 localizes to the endoplasmic reticulum (ER) membrane and the nuclear envelope, and therefore must function in these regions.[18] TMEM33 exogenously suppresses reticulon 4C function, which is a protein that induces the formation of the tubular structure of the ER. [18] Therefore, TMEM33 is thought to regulate tubular ER structure through modulation of reticulon activity. Tts1, TMEM33 ortholog in S. pombe, has been found to be involved in dictating ER curvature as well.[19] In the nucleus, knock-out studies indicate Tts1 has a role in directing the spindle pole bodies and nuclear core complexes in the nuclear envelope during mitosis. [19]

References

  1. 1 2 "Gene: Transmembrane protein 33". Retrieved 2014-02-25.
  2. ↑ "TMEM33". GeneCards Human Gene Database.
  3. 1 2 "USCS Genome Bioinformatics". Retrieved 2015-04-05.
  4. ↑ "NCBI GEO profile". Retrieved 2015-04-05.
  5. ↑ "NCBI UniGene EST profile TMEM33". Retrieved 2015-04-15.
  6. 1 2 3 4 "Genomatix: ElDorado". Retrieved 2015-04-15.
  7. 1 2 3 "NCBI Aceview: TMEM33". Retrieved 2015-04-05.
  8. ↑ "NCBI Nucleotide: Homo sapiens transmembrane protein 33 (TMEM33) mRNA". Retrieved 2015-02-15.
  9. ↑ "ExPASy: SUSIO". Retrieved 2015-04-05.
  10. ↑ "NCBI Aceview TMEM33". Retrieved 2015-04-05.
  11. 1 2 3 "NCBI Protein: Homo sapiens transmembrane protein 33". Retrieved 2015-02-05.
  12. 1 2 3 "PSORTII Server". Retrieved 2015-04-22.
  13. ↑ "Gene cards: TMEM33". Retrieved 2015-03-09.
  14. 1 2 3 "San Diego Super Computer: isoelectric point determination". Retrieved 2015-04-19.
  15. ↑ "NetPhos 2.0". Retrieved 2015-04-12.
  16. ↑ "NetPhosK 1.0". Retrieved 2015-04-12.
  17. ↑ "NetOGlyc 4.0". Retrieved 2015-04-12.
  18. 1 2 3 4 "Identification and Characterization of TMEM33 as a Reticulon-binding Protein" (PDF). Retrieved 2015-02-22.
  19. 1 2 3 "Tts1, the fission yeast homologue of the TMEM33 family, functions in NE remodeling during mitosis". Retrieved 2015-02-22.
  20. 1 2 "NCBI: BLAST". Retrieved 2015-03-22.
  21. ↑ "Biogrid protein interactions with TMEM33". Retrieved 2015-04-17.
  22. ↑ "The Two-pore channel (TPC) interactome unmasks isoform-specific roles for TPCs in endolysosomal morphology and cell pigmentation". Retrieved 2015-02-22.

Further reading

  • Urade, Takeshi; et al. (2014). "Identification and Characterization of TMEM33 as a Reticulon-binding Protein. Online.". Kobe Journal of Medical Sciences 60 (3): 57–65. 
  • Zhang, D; Oliferenko, S (2014). "Tts1, the fission yeast homologue of the TMEM33 family, functions in NE remodeling during mitosis". Molecular Biology of the Cell 25 (19): 2970–83. doi:10.1091/mbc.E13-12-0729. PMC 4230586. PMID 25103238. 
  • Chi, A; Valencia, J. C.; Hu, Z. Z.; Watabe, H; Yamaguchi, H; Mangini, N. J.; Huang, H; Canfield, V. A.; Cheng, K. C.; Yang, F; Abe, R; Yamagishi, S; Shabanowitz, J; Hearing, V. J.; Wu, C; Appella, E; Hunt, D. F. (2006). "Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes". Journal of Proteome Research 5 (11): 3135–44. doi:10.1021/pr060363j. PMID 17081065. 
  • Scifo, E; Szwajda, A; Dębski, J; Uusi-Rauva, K; Kesti, T; Dadlez, M; Gingras, A. C.; Tyynelä, J; Baumann, M. H.; Jalanko, A; Lalowski, M (2013). "Drafting the CLN3 protein interactome in SH-SY5Y human neuroblastoma cells: A label-free quantitative proteomics approach". Journal of Proteome Research 12 (5): 2101–15. doi:10.1021/pr301125k. PMID 23464991. 
  • Daulat, A. M.; Maurice, P; Froment, C; Guillaume, J. L.; Broussard, C; Monsarrat, B; Delagrange, P; Jockers, R (2007). "Purification and identification of G protein-coupled receptor protein complexes under native conditions". Molecular & Cellular Proteomics 6 (5): 835–44. doi:10.1074/mcp.M600298-MCP200. PMID 17215244. 
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