TMEM128

Last updated

TMEM128
Identifiers
Aliases TMEM128 , transmembrane protein 128
External IDs MGI: 1913559; HomoloGene: 11944; GeneCards: TMEM128; OMA:TMEM128 - orthologs
Orthologs
SpeciesHumanMouse
Entrez

85013

66309

Ensembl

ENSG00000132406

ENSMUSG00000067365

UniProt

Q5BJH2

Q9CZB9

RefSeq (mRNA)

NM_001297551
NM_001297552
NM_032927

NM_025480
NM_001356960

RefSeq (protein)

NP_001284480
NP_001284481
NP_116316

NP_079756
NP_001343889

Location (UCSC) Chr 4: 4.24 – 4.25 Mb Chr 5: 38.42 – 38.43 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

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. [5] TMEM128 contains four transmembrane domains and is localized in the Endoplasmic Reticulum membrane. [6] [7] [8] 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.

Contents

Gene

The TMEM128, or transmembrane protein 128, gene in humans is located on the minus strand at 4p16.3. [9] TMEM128 contains 5 exons total and is 12,701 base pairs long including introns. [5] [9] [10]

Transcripts

There are two isoforms of TMEM128. [11] Isoform 1 being the longest, consists of two variants differing in the 3' UTR region. [11] Variant 1 mRNA is 1,243 base pairs long while Variant 2 mRNA is 1,241 base pairs long. [5] [12] Isoform 2 differs in the 5' UTR region of the protein and uses a different start codon location compared to the first variant. [11] This variant is longer at 1,785 base pairs and has a different N-terminus. [13]

Neighboring genes

TMEM128 is neighbored upstream by LYAR , Ly1 antibody reactive, and downstream by OTOP1, Otopetrin 1. [14]

Protein

Isoform 1

TMEM128 Isoform 1 translates into a protein of 165 amino acids long, containing four transmembrane domains. [6] These domains exist at amino acids 49-69, 81-101, 119-139, and 144-164. [6] Isoform 1 is18,882 Da and has a pI of 6.27. [15] Using compositional analysis, the amino acid composition is similar to the average protein and there are no significant repeats in the protein. [15]

Predicted Secondary Structure for TMEM128 TMEM128 membrane domains.png
Predicted Secondary Structure for TMEM128

Isoform 2

Isoform 2 translates into a protein of 141 amino acids long, also containing four transmembrane domains. [17] [18] Isoform 2 has a different molecular weight and isoelectric point compared to Isoform 1, coming in at 16,093 Da and having a pI of 6.8. [15]

Secondary structure

Secondary structure composition
Type of secondary structureNumber of amino acidsPercent composition
Alpha helix 3420.61%
Extended strand5935.76%
Random coil 7243.64%

Predicted secondary structure composition shows that most of the secondary structure consists of random coils. [19] No disulfide bonds are predicted to be present. [20]

Membrane topology of TMEM128 shows the four transmembrane domains, longer N-terminus, and shorter C terminus.

Tertiary structure

Predicted Tertiary Structure of TMEM128 as predicted by I-TASSER Tertiary Structure of TMEM128.jpg
Predicted Tertiary Structure of TMEM128 as predicted by I-TASSER
Predicted 3-D structure of TMEM128 as predicted by PHYRE2 TMEM128.png
Predicted 3-D structure of TMEM128 as predicted by PHYRE2

Tertiary structure is predicted to have four spiral domains in TMEM128. These domains are the transmembrane sections of the protein. For the above models, it is colored rainbow from N-terminus to C-terminus.

Regulation of expression

Gene level regulation

TMEM128 mRNA expression by tissue type in humans NCBI GEO TMEM128 Differential Expression by Tissue.png
TMEM128 mRNA expression by tissue type in humans

Several promotors/enhancers of TMEM128 exist, with the GH04J00427 promotor located near the start of transcription, the GH04J004540 enhancer located downstream, and GH04J004264 enhancer located upstream of their target gene. [9] [14] TMEM128 sequence also contains many binding sites for various transcription factors, including TATA box, CCAAT binding protein, and cAMP-responsive element binding protein. [23]

Expression of TMEM128 is also regulated at the gene level through differential tissue expression as seen with the image to the left. Red bars represent absolute expression while blue dots represent relative expression. TMEM128 is expressed highly in areas such as the adrenal gland and spinal cord, while is lower in areas such as the liver and bone marrow. [11]

Transcript level regulation

Predicted stem loops for 3' UTR of TMEM128 Secondary structure for 3' UTR of TMEM128.png
Predicted stem loops for 3' UTR of TMEM128
TMEM128 RNA expression in a mouse brain RNA Expression of TMEM128 in a mouse brain.png
TMEM128 RNA expression in a mouse brain

Several miRNAs have binding sites on the 3' UTR of TMEM128 including: [26]

These miRNAs can participate in RNA silencing to prevent the expression of the mRNA.

Analyses of mouse brains show lack of region-specific expression throughout. [25]

Protein level regulation

In terms of protein regulation, TMEM128 contains many different post-translational domains including glycation, [27] phosphorylation, [28] SUMOylation, [29] and O-GlcNAc [30] as seen below:

ModificationAmino acid number
Phosphorylation3, 4, 52, 124, 135, 162
Glycation70, 73, 115
Nuclear export signal [31] 88-95
SUMOylation39-42, 115-118, 161-165
O-GlcNAc3, 4, 34, 35, 123
Acetylation [32] 40, 41, 43, 73

Post-translational modification alters protein structure and can thus alter protein function and viability.

Sub-cellular localization

TMEM128 was found to be located in the Endoplasmic Reticulum membrane, with the N-terminus and C-terminus facing into the cytoplasm. [7] [8]

Evolution

Paralogs

There are no known paralogs of TMEM128. [33]

Orthologs

Orthologs of TMEM128 have not been found outside of Eukaryotes. [33] Inside of Eukaryotes, TMEM128 orthologs have been found in mammals, birds, and several fungi. Mammals contained the highest amount of conservation at no less than 71% conservation. The most distant ortholog detected was the Diversispora epigaea, a fungus. The transmembrane domains of this protein remain the most conserved throughout species, with key amino acids Trp51, Trp139, and Trp142 being conserved in all species with orthologous proteins. All information below was obtained through NCBI BLAST. [33]

Orthologs of TMEM128
Genus and SpeciesCommon NameDate of Divergence (MYA) [34] Accession numberSequence lengthSequence identity
Homo sapiens Human0NP_001284480.1165100%
Rhinopithecus roxellana Golden snub-nosed monkey28.81XP_010355887.216597%
Mus musculus House mouse89NP_001343889.116381%
Microtus ochrogaster Prairie vole89XP_00536602116480%
Ovis aries Sheep94XP_014952114.216583%
Vulpes vulpes Red fox94XP_025854088.116582%
Pteropus vampyrus Large flying fox94XP_011372965.116581%
Orcinus orca Killer whale94XP_004269680.116581%
Monodelphis domestica Gray short-tailed opossum160XP_001371407.317071%
Taeniopygia guttata Zebra finch318XP_002193492.317368%
Alligator sinensis Chinese alligator318XP_006016834.117267%
Pogona vitticeps Central bearded dragon318XP_020633929.116362%
Xenopus laevis African clawed frog351.7NP_001084889.116652%
Orbicella faveolata Mountainous star coral687XP_020610022.117138%
Exaiptasia pallida Sea anenmone687XP_028518835.116936%
Octopus vulgaris Common octopus736XP_029645279.118433%
Brachionus plicatilis N/A736RNA25638.117028%
Crassostrea virginica Eastern oyster736XP_022343076.120028%
Diversispora epigaea N/A1017RHZ70611.117624%

Mutation rate

Divergence of TMEM128 Relative to Fibrinogen Alpha Chain and Cytochrome C Divergence of TMEM128.jpg
Divergence of TMEM128 Relative to Fibrinogen Alpha Chain and Cytochrome C

The evolution rate is at a medium pace, slower than the fibrinogen alpha chain but faster than cytochrome c, suggesting neither positive or negative selection at this locus.

Interacting proteins

TMEM128 has been found via yeast two-hybrid assays to interact with:

Function

The biological function of TMEM128 is still poorly understood. As this is a transmembrane protein, common functions may include receptors, channels, or anchorage. [40] Because TMEM128 has post-translational modification sites, alternative protein states may be present that permit TMEM128 to have different forms. For example, phosphorylation of TMEM128 may make it bind to different substrates through conformational change. [41] TMEM128 also has a variety of interactions with other proteins as discussed above, suggesting it may have a broad range of action.

Clinical significance

Cancer

TMEM128 has been found to show moderate to strong positivity in some patients with carcinoma, with other types of cancer such as melanoma, glioma, breast, ovarian, renal, and pancreatic showing weak to moderate positivity. [42] TMEM128 also has been found to show low cancer specificity. [42]

Skeletal muscle

TMEM128 expression is experimentally associated with presence of the ROR alpha1 protein, as TMEM128 was found in lower quantities when ROR alpha1 was deleted. [43] [44]

Skin

TMEM128 expression was lowered following a null mutation of TAp63 in skin cells. [45] [46]

Cardiac muscle

TMEM128 expression was increased following a Trypanosoma cruzi infection. [47] [48]

Neurological diseases

While it has been associated with several diseases such as Wolf-Hirschhorn Syndrome, no evidence exists for the exact cause of this syndrome and may only be correlation because of location on chromosome 4 [9] [49]

Mutations

Several SNPs have been found in association with TMEM128: [50]

Key SNPs of TMEM128
mRNA positionAmino acid positiondbSNP rs#Reference alleleSNP alleleFunction
16943rs771177507ACMissense
18649rs146625911ACMissense
20455rs1434953873GTMissense
27077rs13135886AGMissense
463139rs757745482TCMissense
466142rs1213450146GANonsense
512158rs202215273GA, TMissense

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References

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  47. ↑ "GDS5112 / 1448317_at". www.ncbi.nlm.nih.gov. Retrieved May 2, 2020.
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  49. ↑ Yang WX, Pan H, Li L, Wu HR, Wang ST, Bao XH, et al. (March 2016). "Analyses of Genotypes and Phenotypes of Ten Chinese Patients with Wolf-Hirschhorn Syndrome by Multiplex Ligation-dependent Probe Amplification and Array Comparative Genomic Hybridization". Chinese Medical Journal. 129 (6): 672–8. doi: 10.4103/0366-6999.177996 . PMC   4804413 . PMID   26960370.
  50. ↑ "SNP linked to Gene (geneID:85013) Via Contig Annotation". www.ncbi.nlm.nih.gov. Retrieved May 2, 2020.
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