TEDDM1

Last updated
TEDDM1
Identifiers
Aliases TEDDM1 , EDDM9, Epdd1, HE9, TMEM45C, HEL-S-45e, transmembrane epididymal protein 1
External IDs MGI: 3646829 HomoloGene: 131186 GeneCards: TEDDM1
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_172000

NM_001008426

RefSeq (protein)

NP_741997

NP_001008426

Location (UCSC) Chr 1: 182.4 – 182.4 Mb Chr 1: 153.75 – 153.75 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Transmembrane epididymal protein 1 is a transmembrane protein encoded by the TEDDM1 gene. TEDDM1 is also commonly known as TMEM45C and encodes 273 amino acids that contains six alpha-helix transmembrane regions. The protein contains a 118 amino acid length family of unknown function. While the exact function of TEDDM1 is not understood, it is predicted to be an integral component of the plasma membrane. [5]

Contents


Gene

Locus

TEDDM1 is located on chromosome 1 found at 1q25.3 on the minus end. TEDDM1 is composed of a single exon. The gene neighborhood of TEDDM1 includes glutamate-ammonia ligase (GLUL), long intergenic non-protein coding RNA 272 (LINC00272), and Sharpr-MPRA regulatory region 13543 (LOC122149321). [6] [7] [8]

Location of TEDDM1 on Chromosome 1. TEDDM1-gene.png
Location of TEDDM1 on Chromosome 1.

Expression

Allen Brain Atlas depiction of TEDDM1 expression in Mus musculus using an RNA probe. TEDDM! Mus musculus.png
Allen Brain Atlas depiction of TEDDM1 expression in Mus musculus using an RNA probe.

TEDDM1 is expressed in most major tissues. The gene is expressed at a high level in the testis and a low level in the heart relative to all other tissues with TEDDM1 expression. [9] In the brain, TEDDM1 is expressed in the amygdala, the hippocampus, and the striatum. In the mouse brain, TEDDM1 was discovered with general expression using an RNA probe. [10]

Within the cell, TEDDM1 is primarily expressed in the plasma membrane. Similar to other membrane-bound proteins, TEDDM1 protein contains a predicted signal peptide, although the type of signal peptide is unknown. [11] Because TEDDM1 shares many characteristics with other transmembrane proteins, this suggests that the protein may have a role in various cell processes like signal transduction and protein trafficking. [12]

Gene Level Regulation

The expression pattern of TEDDM1 was ubiquitous. TEDDM1 mRNA abundance was moderate to low in humans. [13]

Protein

The molecular weight of the TEDDM1 protein is approximately 31.3 kDa and the theoretical isoelectric point (pI) of TEDDM1 is 8.02. Notably, this is different than the average pI of other proteins as their pI land in the pH range of 4-7. [14] This suggests that TEDDM1 protein contains an excess of basic amino acids relative to most proteins. [15]

Domains

TEDDM1 has a single major domain of unknown function entitled DUF716. This domain spans from amino acid position 95 to 219 of the protein. DUF716 contains the majority of a leucine zipper which is typically associated with dimerization of the protein. DUF716 also contains three of the six transmembrane regions in the protein, and contains amino acid segments of high conservation, suggesting DUF716 likely plays an important role in TEDDM1 protein function. [16]

Post Translational Modifications

TEDDM1 is subject to several post translational modifications. There are eighteen predicted phosphorylation sites. Other specific sites include an N-glycosylation site, a casein kinase II phosphorylation site, a Leucine zipper pattern, two N-myristylation sites, and three protein kinase C phosphorylation sites. N-glycosylation is another typical feature of membrane proteins and is involved in secretion and cytoskeletal organization. [17] Casein kinase II is involved with protein stability and cell signaling response. [18] Leucine zippers are sequence motifs that facilitate protein-protein interactions. [19] N-myristylation sites are involved in ligand binding and protein dynamics. [20] Protein kinase C phosphorylation has to do with regulation of cell proliferation and gene expression. [21]

Structure

Alphafold depiction of the tertiary structure of TEDDM1. Alphafold TEDDM1.png
Alphafold depiction of the tertiary structure of TEDDM1.

The secondary structure of TEDDM1 begins with free random coils at the N-terminus and a single alpha helix. The six transmembrane proteins in TEDDM1 are characterized as structurally similar alpha helices. This region of the protein is quite condensed relative to the N-terminus. [22] Alpha helices typically have mainly hydrophobic residues, which aligns with these regions being located within the plasma membrane. Alpha helices are also commonly associated with DNA binding motifs. [23]

Homology/Evolution

Paralogs

TEDDM1 has two known paralogs, TMEM45A and TMEM45B. [24] [25]

Orthologs

Over 100 orthologs exist for human gene TEDDM1. Of these known orthologs they were found only to exist in mammals, amphibians, and fish.The divergence date of all orthologs found were compared relative to Homosapiens . Fish TEDDM1 are the most distantly related orthologs to Human TEDDM1, with the furthest median date of divergence being 464 million years ago. While orthologs for TEDDM1 exist in bony fish, as evidenced by its existence in Protopterus annectens , orthologs of the gene were far more frequently found in cartilaginous fish. [26]

Seq #TEDDM1Genus, SpeciesCommon NameTaxonomic OrderDivergence Date (MYA)Accession NumberQuery CoverSequence Length (aa)Sequence Identity (%)Sequence Similarity (%)
1MammalsHomo sapienshumanPrimate0NP_741997.3100273100100
2Nannospalax galilimiddle east blind mole-ratRodentia89XP_008836723.11003057174
3Gracilinanus agilisagile gracile opossumDidelphimorphia160XP_044531579.1802953549
4Tachyglossus aculeatusshort beaked echidnaTachyglossidae180XP_038601041.1822953750
5AmphibiansXenopus tropicaliswestern clawed frogPipidae353XP_017949911.1822843243
6Geotrypetes seraphinigaboon caecelianDermorphiidae353XP_033814670.1703083628
7Rhinatrema bivittatumtwo-lined caecelianGymnophiona353XP_029473035.1773053647
8Nanorana parkerihigh himalaya frogDicroglossidae353XP_018432032.1802643044
9FishProtopterus annectenswest african lungfishProtopteridae408XP_043932144.1863083444
10Amblyraja radiatathorny skateRajidae464XP_032887195.1583144747
11Callorhinchus miliielephant sharkHolocephali464XP_007900619.1753003646
12Carcharodon carchariasgreat white sharkChondrichthyes464XP_041060943.1813063948

Evolution

TEDDM1 molecular evolution rate relative to Fibrinogen Alpha and Cytochrome C. EXCEL.png
TEDDM1 molecular evolution rate relative to Fibrinogen Alpha and Cytochrome C.

The relative rate of molecular evolution of TEDDM1 was quite similar to that of Fibrinogen Alpha and much more rapid than the evolution rate of Cytochrome C.

Interacting Proteins

Predicted functional partners to the TEDDM1 protein found via STRING. [27]

ProteinDescriptionFunction
SBK2Serine/threonine-protein kinase 2Predicted to be involved in MAPK cascade and protein phosphorylation
METTL7BMethyltransferase-like protein 7BProbable methyltransferase
PATE2Prostate and testis expressed 2Contain LY6/PLAUR domain in extracellular space
ODF3L1Outer dense fiber protein 3-like protein 1Active in cytoskeleton
DEFB30Beta-defensin 130a; Defensin, beta 130Antimicrobial host-defense peptide, antiplasmodial activity
SPINT3Serine peptidase inhibitor, Kunitz type 3Enable receptor antagonist activity and beta binding activity
TSPAN1Tetraspanin-1Mediate signal transduction events, role in the regulation of cell development, growth
WFDC10AWap four-disulfide core domain protein 10aFunctions as a protease inhibitor
EDDM3BEpididymal secretory protein E3-betaPossible function in sperm maturation

Clinical Significance

According to previous cancer research studies, gene-based association analyses discovered that TEDDM1 along with GLUL are the two genes most significantly correlated with hepatitis B virus related hepatocellular carcinoma, the most common form of liver cancer. [28] TEDDM1 also has significant clinical significance due to its involvement with keratinocytes and the inhibition of microRNA-31, an important regulator of embryonic implantation and development. [29]

Related Research Articles

<span class="mw-page-title-main">TMEM242</span> Protein-coding gene in the species Homo sapiens

Transmembrane protein 242 (TMEM242) is a protein that in humans is encoded by the TMEM242 gene. The tmem242 gene is located on chromosome 6, on the long arm, in band 2 section 5.3. This protein is also commonly called C6orf35, BM033, and UPF0463 Transmembrane Protein C6orf35. The tmem242 gene is 35,238 base pairs long, and the protein is 141 amino acids in length. The tmem242 gene contains 4 exons. The function of this protein is not well understood by the scientific community. This protein contains a DUF1358 domain.

TMEM143 is a protein that in humans is encoded by TMEM143 gene. TMEM143, a dual-pass protein, is predicted to reside in the mitochondria and high expression has been found in both human skeletal muscle and the heart. Interaction with other proteins indicate that TMEM143 could potentially play a role in tumor suppression/expression and cancer regulation.

<span class="mw-page-title-main">PRR29</span> Protein-coding gene in the species Homo sapiens

PRR29 is a protein encoded by the PRR29 gene located in humans on chromosome 17 at 17q23.

<span class="mw-page-title-main">RTL6</span>

Retrotransposon Gag Like 6 is a protein encoded by the RTL6 gene in humans. RTL6 is a member of the Mart family of genes, which are related to Sushi-like retrotransposons and were derived from fish and amphibians. The RTL6 protein is localized to the nucleus and has a predicted leucine zipper motif that is known to bind nucleic acids in similar proteins, such as LDOC1.

<span class="mw-page-title-main">Transmembrane protein 44</span>

Transmembrane protein 44 is a protein that in humans is encoded by the TMEM44 gene.

<span class="mw-page-title-main">TMEM44</span> Protein-coding gene in the species Homo sapiens

TMEM44 is a protein that in humans is encoded by the TMEM44 gene. DKFZp686O18124 is a synonym of TMEM44.

<span class="mw-page-title-main">TMEM125</span> Protein

Transmembrane protein 125 is a protein that, in humans, is encoded by the TMEM125 gene. It has 4 transmembrane domains and is expressed in the lungs, thyroid, pancreas, intestines, spinal cord, and brain. Though its function is currently poorly understood by the scientific community, research indicates it may be involved in colorectal and lung cancer networks. Additionally, it was identified as a cell adhesion molecule in oligodendrocytes, suggesting it may play a role in neuron myelination.

<span class="mw-page-title-main">TMEM128</span>

TMEM128, also known as Transmembrane Protein 128, is a protein that in humans is encoded by the TMEM128 gene. TMEM128 has three variants, varying in 5' UTR's and start codon location. TMEM128 contains four transmembrane domains and is localized in the Endoplasmic Reticulum membrane. TMEM128 contains a variety of regulation at the gene, transcript, and protein level. While the function of TMEM128 is poorly understood, it interacts with several proteins associated with the cell cycle, signal transduction, and memory.

<span class="mw-page-title-main">LSMEM2</span> Protein-coding gene in the species Homo sapiens

Leucine rich single-pass membrane protein 2 is a single-pass membrane protein rich in leucine, that in humans is encoded by the LSMEM2 gene. The LSMEM2 protein is conserved in mammals, birds, and reptiles. In humans, LSMEM2 is found to be highly expressed in the heart, skeletal muscle and tongue.

<span class="mw-page-title-main">TMEM221</span> Protein

Transmembrane protein 221 (TMEM221) is a protein that in humans is encoded by the TMEM221 gene. The function of TMEM221 is currently not well understood.

TMEM275 is a protein that in humans is encoded by the TMEM275 gene. TMEM275 has two, highly-conserved, helical trans-membrane regions. It is predicted to reside within the plasma membrane or the endoplasmic reticulum's membrane.

Transmembrane protein 39B (TMEM39B) is a protein that in humans is encoded by the gene TMEM39B. TMEM39B is a multi-pass membrane protein with eight transmembrane domains. The protein localizes to the plasma membrane and vesicles. The precise function of TMEM39B is not yet well-understood by the scientific community, but differential expression is associated with survival of B cell lymphoma, and knockdown of TMEM39B is associated with decreased autophagy in cells infected with the Sindbis virus. Furthermore, the TMEM39B protein been found to interact with the SARS-CoV-2 ORF9C protein. TMEM39B is expressed at moderate levels in most tissues, with higher expression in the testis, placenta, white blood cells, adrenal gland, thymus, and fetal brain.

C2orf74, also known as LOC339804, is a protein encoding gene located on the short arm of chromosome 2 near position 15 (2p15). Isoform 1 of the gene is 19,713 base pairs long. C2orf74 has orthologs in 135 different species, including primarily placental mammals and some marsupials.

<span class="mw-page-title-main">FAM98C</span> Gene

Family with sequence 98, member C or FAM98C is a gene that encodes for FAM98C has two aliases FLJ44669 and hypothetical protein LOC147965. FAM98C has two paralogs in humans FAM98A and FAM98B. FAM98C can be characterized for being a Leucine-rich protein. The function of FAM98C is still not defined. FAM98C has orthologs in mammals, reptiles, and amphibians and has a distant orhtologs in Rhinatrema bivittatum and Nanorana parkeri.

<span class="mw-page-title-main">C11orf98</span> Protein-coding gene in the species Homo sapiens

C11orf98 is a protein-encoding gene on chromosome 11 in humans of unknown function. It is otherwise known as c11orf48. The gene spans the chromosomal locus from 62,662,817-62,665,210. There are 4 exons. It spans across 2,394 base pairs of DNA and produces an mRNA that is 646 base pairs long.

<span class="mw-page-title-main">TMEM212</span> Protein-coding gene in the species Homo sapiens

Transmembrane protein 212 is a protein that in humans is encoded by the TMEM212 gene. The protein consists of 5 transmembrane domains and localizes in the plasma membrane and endoplasmic reticulum. TMEM212 has orthologs in vertebrates but not invertebrates. TMEM212 has been associated with sporadic Parkinson's disease, facial processing, and adiposity in African Americans.

<span class="mw-page-title-main">TMEM104</span> TMEM104 protein encoding gene

Transmembrane protein 104 (TMEM104) is a protein that in humans is encoded by the TMEM104 gene. The aliases of TMEM104 are FLJ00021 and FLJ20255. Humans have a 163,255 base pair long gene coding sequence, 4703 base pair long mRNA, and 496 amino acid long protein sequence. In Eukaryotes, the TMEM104 gene is conserved.

<span class="mw-page-title-main">C13orf46</span> C13of46 Gene and Protein

Chromosome 13 Open Reading Frame 46 is a protein which in humans is encoded by the C13orf46 gene. In humans, C13orf46 is ubiquitously expressed at low levels in tissues, including the lungs, stomach, prostate, spleen, and thymus. This gene encodes eight alternatively spliced mRNA transcript, which produce five different protein isoforms.

<span class="mw-page-title-main">TMEM248</span> Transmembrane protein 248/TMEM248 gene

Transmembrane protein 248, also known as C7orf42, is a gene that in humans encodes the TMEM248 protein. This gene contains multiple transmembrane domains and is composed of seven exons.TMEM248 is predicted to be a component of the plasma membrane and be involved in vesicular trafficking. It has low tissue specificity, meaning it is ubiquitously expressed in tissues throughout the human body. Orthology analyses determined that TMEM248 is highly conserved, having homology with vertebrates and invertebrates. TMEM248 may play a role in cancer development. It was shown to be more highly expressed in cases of colon, breast, lung, ovarian, brain, and renal cancers.

<span class="mw-page-title-main">TMEM271</span> TMEM271 gene and protein

Transmembrane protein 271, or TMEM271 is a protein in Homo sapiens encoded by the TMEM271 gene, located at 4p16.3 on the minus strand. The protein is located on the plasma membrane of cells and highly expressed in several regions of the brain.

References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000203730 - Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000043282 - Ensembl, May 2017
  3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. "TEDDM1 transmembrane epididymal protein 1 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2022-07-28.
  6. "GLUL glutamate-ammonia ligase [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2022-07-28.
  7. "LINC00272 long intergenic non-protein coding RNA 272 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2022-07-28.
  8. "LOC122149321 Sharpr-MPRA regulatory region 13543 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2022-07-28.
  9. "TEDDM1 Gene - GeneCards | TEDM1 Protein | TEDM1 Antibody". www.genecards.org. Retrieved 2022-07-28.
  10. "Experiment Detail :: Allen Brain Atlas: Mouse Brain". mouse.brain-map.org. Retrieved 2022-07-30.
  11. "Services". healthtech.dtu.dk. Retrieved 2022-07-30.
  12. Attwood MM, Schiöth HB (2021). "Characterization of Five Transmembrane Proteins: With Focus on the Tweety, Sideroflexin, and YIP1 Domain Families". Frontiers in Cell and Developmental Biology. 9: 708754. doi: 10.3389/fcell.2021.708754 . PMC   8327215 . PMID   34350187.
  13. "PAXdb: Protein Abundance Database". pax-db.org. Retrieved 2022-07-30.
  14. Novák P, Havlíček V (January 2016). "Protein extraction and precipitation.". Proteomic profiling and analytical chemistry. Elsevier. pp. 51–62. doi:10.1016/B978-0-444-63688-1.00004-5. ISBN   978-0-444-63688-1. The pI of most proteins is in the pH range of 4 to 7.
  15. "Compute pI/MW - SIB Swiss Institute of Bioinformatics | Expasy". www.expasy.org. Retrieved 2022-07-28.
  16. "Motif Scan". myhits.sib.swiss. Retrieved 2022-07-30.
  17. Kukuruzinska MA, Lennon K (1998). "Protein N-glycosylation: molecular genetics and functional significance". Critical Reviews in Oral Biology and Medicine. 9 (4): 415–448. doi: 10.1177/10454411980090040301 . PMID   9825220.
  18. Litchfield DW, Lüscher B (November 1993). Khandelwal RL, Wang JH (eds.). "Casein kinase II in signal transduction and cell cycle regulation". Molecular and Cellular Biochemistry. Boston, MA: Springer US. 127–128: 187–199. doi:10.1007/978-1-4615-2600-1_18. ISBN   978-1-4615-2600-1. PMID   7935350.
  19. Landschulz WH, Johnson PF, McKnight SL (June 1988). "The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins". Science. 240 (4860): 1759–1764. Bibcode:1988Sci...240.1759L. doi:10.1126/science.3289117. PMID   3289117.
  20. Bastidas AC, Pierce LC, Walker RC, Johnson DA, Taylor SS (September 2013). "Influence of N-myristylation and ligand binding on the flexibility of the catalytic subunit of protein kinase A". Biochemistry. 52 (37): 6368–6379. doi:10.1021/bi400575k. PMC   3788587 . PMID   24003983.
  21. Lim PS, Sutton CR, Rao S (December 2015). "Protein kinase C in the immune system: from signalling to chromatin regulation". Immunology. 146 (4): 508–522. doi:10.1111/imm.12510. PMC   4693901 . PMID   26194700.
  22. "AlphaFold Protein Structure Database". alphafold.ebi.ac.uk. Retrieved 2022-07-30.
  23. Rutherford K, Van Duyne GD (2013). "DNA Sequence Recognition by Proteins.". In Lennarz WJ, Lane MD (eds.). Encyclopedia of Biological Chemistry (Second ed.). London: Academic Press. ISBN   978-0-12-378631-9. The α-helix is the structural element most frequently used for sequence-specific interactions in protein–DNA interfaces. The size of an α-helix matches the width of the DNA major groove, allowing them to fit together tightly while the protein side chains on the helix probe the available base-pair functional groups.
  24. "TMEM45A transmembrane protein 45A [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2022-07-28.
  25. "TMEM45B transmembrane protein 45B [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2022-07-28.
  26. "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2022-07-28.
  27. "TEDDM1 protein (human) - STRING interaction network". string-db.org. Retrieved 2022-07-28.
  28. Lin YY, Yu MW, Lin SM, Lee SD, Chen CL, Chen DS, Chen PJ (October 2017). "Genome-wide association analysis identifies a GLUL haplotype for familial hepatitis B virus-related hepatocellular carcinoma". Cancer. 123 (20): 3966–3976. doi:10.1002/cncr.30851. PMID   28662289. S2CID   25961704.
  29. Stepicheva NA, Song JL (August 2016). "Function and regulation of microRNA-31 in development and disease". Molecular Reproduction and Development. 83 (8): 654–674. doi:10.1002/mrd.22678. PMC   6040227 . PMID   27405090.