Transmembrane protein 89

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Transmembrane protein 89 (TMEM89) is a protein that in humans is encoded by the TMEM89 gene.

Gene

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Structure

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The TMEM89 gene is found on the minus strand of chromosome 3 (3p21.31) from 48,658,192 to 48,659,288 and is 1,011 nucleotides long.[1][2] The gene has two exons.[1][2] These two exons are not predicted to be alternatively spliced.[1][2]

Gene expression

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The TMEM89 gene is most highly expressed in the testis.[1][2] TMEM89 is also found to be expressed at low levels in other tissues such as the stomach, kidneys, heart, ovaries, thyroid, colon, bone marrow, and in adrenal tissues.[1] This gene is also expressed in fetal heart, stomach, kidney, and intestine tissues.[1] Immunohistochemistry data has also found TMEM89 located in the cell membranes of the colon, fallopian tube, kidney, and testis tissues.[3][4] Expression of the TMEM89 gene has also been found in low amounts in the brain tissue from a mouse cerebellum.[5]

Gene expression neighborhood

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Human TMEM89 is a part of the Human Protein Atlas expression cluster 23: SpermatidS - Flagellum & Golgi organization.[3][6] The 15 closest expression neighbors include OR4M1, ANTXRL, TGIF2LX, CPXCR1, C3orf84, CXorf66, CLDN17, C11orf94, USP50, SPDYE4, MMP20, SSMEM1, SPMAP1, SPACA1, and LYZL1.[6]

Differential gene expression

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TMEM89 expression is much higher in amniotic fluid derived hAKPC-P cells compared with immortalized hIPod line cells.[7] TMEM89 expression is higher in cells that have macrophage migration inhibitory factor (MIF) knocked down compared to the control.[8] TMEM89 expression is the lowest in cardiomyocytes from human embryonic stem cells, compared to expression in human embryonic stem cells, embryoid bodies with beating cardiomyocytes, and cardiomyocytes from fetal hearts.[9]

Clinical significance

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Gene expression of TMEM89 was found to be upregulated in upper tract urothelial carcinomas, and therefore predicted as a possible biomarker secretory protein for these types of carcinomas.[10] The TMEM89 gene was found to be a potential modifier of autism spectrum disorder severity in a SNP analysis.[citation needed] Gene expression of TMEM89 was also used in a model that predicted the risk score for a potential relapse in stage 1 testicular germ cell tumors.[11]

File:Wiki concep trans-1.jpg
Human TMEM89 Conceptual Translation[1][12][13][14][15][16][17]

Protein

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Structure

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Primary

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The human TMEM89 protein is 159 amino acids long.[1] This protein has a molecular mass of ~17.5kDa and an isoelectric point of ~10 pI.[2][18] Proteins with a more basic pI are usually associated with the mitochondria or the plasma membrane and have fewer protein interactions.[19][20] The protein structure contains two topological domains (extracellular and cytoplasmic) and a helical transmembrane domain.[13][21][22] The human TMEM89 protein is rich in the amino acids histidine, leucine, and tryptophan.[14] The amino acids aspartate, asparagine, and phenylalanine are present in low amounts in the human TMEM89 protein.[14] Amino acid patterns such as ED are present in the human TMEM89 protein at low amounts, while the pattern KR-ED is present in high amounts.[14] Within the extracellular domain of the human TMEM89 protein, there are 3 cysteines with regular spacing.[14] In the cytoplasmic domain, there are two positive amino acid runs from amino acids 3-5 and 25-27.[14] These different amino acid patterns and protein domains can be visualized in the figures to the right.

File:TMEM89 hydrophobicity.jpg
Human TMEM89 SOSUI Hydrophobicity and Net Charge Density Graph[21]
File:TMEM89 TM wheel.jpg
SOSUI Human TMEM89 Wheel Plot[21]
File:Protter TMM89 HUMAN.png
Protter Human TMEM89 Snake Plot[22]

Secondary

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The TMEM89 protein is only made up of α-helices and strands.[23][24] The α-helices are distributed all throughout the protein in all three domains.[23][24]

Tertiary

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The tertiary structure of Human TMEM89 was predicted using Alphafold and I-Tasser software.[23][24] These structures can be seen on the right.

File:Human TMEM89 Tertiary Structure.jpg
Human TMEM89 Tertiary Structure With Labeled Domains[23][25]
File:Human TMEM89 protein colored by charge.jpg
Human TMEM89 Tertiary Structure with Labeled Charges[25][23]
File:ITasser TMEM89 Signal Peptide and Extracellular Region Prediction.jpg
I-Tasser Human TMEM89 Signal Peptide and Extracellular Domain Structure Prediction[24][25]
File:ITasser and Alphafold TMEM89 singnal peptide and extracellular region comparison.jpg
I-Tasser and Alphafold Human TMEM89 Signal Peptide and Extracellular Domain Comparison[23][24][25]
File:Itasser tmem89 cyt pic.jpg
I-Tasser Human TMEM89 Cytoplasmic Domain Structure Prediction[25][24]
File:Itasser alphafold cyt.jpg
I-Tasser and Alphafold Human TMEM89 Cytoplasmic Domain Comparison[23][25][24]

Post-translational modifications

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The TMEM89 protein has a predicted N-myristylation site from amino acids 47-52, a predicted Src homology 3 (SH3) binding domain from amino acids 106-111, and one conserved predicted phosphorylation site at amino acid S117.[15][17][16] N-myristylation is a protein lipid modification that has roles in protein-protein interactions, cell signaling, and targeting proteins to endomembranes and the plasma membrane.[26] Proteins with SH3 binding domains are usually involved in signal transduction pathways, cytoskeleton organization, membrane trafficking, or organelle assembly.[27] Protein phosphorylation is an important process involved with signal transduction, protein synthesis, cell division, cell growth, development, and aging.[28]

File:PS4 motif schematic.png
Human TMEM89 Motif Schematic[29][15][17][16]
File:TMEM89 N-myristoylation site alignment.png
Human TMEM89 N-myristylation Site Multiple Sequence Alignment[30][15]

Interactions

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The human TMEM89 protein interacts with the proteins C4A, RBM15B, GOLGA6A, PFKFB4, DOCK3, MAPKAPK3, ZNF557, and ZBTB47.[31][32]

Homologs

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Orthologs

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Orthologs of TMEM89 are only found in mammals.[1] The only mammalian taxon that does not contain a TMEM89 ortholog is the monotremes.

Below is a table with information on some of the orthologs of human TMEM89. These orthologs were used to make the multiple sequence alignment and N-myristylation site alignment to the right.

TMEM89 Ortholog Table[33][34][35]
Genus and species Common name Taxon Date of Divergence (MYA) NCBI Accession Number Sequence length (aa) % Identity % Similarity
Homo sapiens Humans Primate 0 NP_001008270.1 159 100 100
Castor canadensis American beaver Rodentia 87 XP_020018275.1 158 73.1 81.2
Urocitellus parryii Arctic ground squirrel Rodentia 87 XP_026239733.1 155 66.0 74.8
Orcinus orca Orca Artiodactyla 94 XP_004283952.1 159 71.9 80.0
Bos taurus Cow Artiodactyla 94 NP_001104538.1 159 63.5 73.5
Odobenus rosmarus divergens Pacific walrus Carnivora 94 XP_004399365.2 159 67.9 77.4
Canis lupus familiaris Dog Carnivora 94 XP_038283783.1 159 65.6 76.2
Talpa occidentalis Spanish mole Eulipotphyla 94 XP_037376292.1 162 66.7 75.3
Condylura cristata Star-nosed mole Eulipotphyla 94 XP_004676653.1 162 63.0 74.1
Pteropus alecto Black flying fox Chiroptera 94 XP_006909233.1 156 65.2 74.5
Desmodus rotundus Common vampire bat Chiroptera 94 XP_024421609.1 159 63.8 74.4
Ceratotherium simum simum Southern white rhinoceros Perissodactyla 94 XP_004419716.1 159 64.2 78.0
Equus caballus Horse Perissodactyla 94 XP_003363167.2 207 49.8 58.9
Manis javanica Malayan pangolin Pholidota 94 KAI5937412.1 158 53.8 67.5
Manis pentadactyla Chinese pangolin Pholidota 94 XP_036733472.1 158 53.1 66.0
Orycteropus afer afer Aardvark Tubulidentata 99 XP_007953489.1 160 68.9 77.0
Loxodonta africana African bush elephant Proboscidea 99 XP_003409726.1 160 68.8 79.4
Dasypus novemcinctus Nine-banded armadillo Cingulata 99 XP_004451990.1 157 67.5 75.0
Sarcophilus harrisii Tasmanian devil Dasyuromorphia 160 XP_031794457.1 168 41.0 52.2
Trichosurus vulpecula Common brushtail possum Diprotodontia 160 XP_036595517.1 168 40.8 51.4
File:PS2 tree image.png
Unrooted Phylogenetic Tree of Human TMEM89 Orthologs[33][36]

Conserved regions

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Regions within the cytoplasmic and extracellular domains of the human TMEM89 protein seem to be the most conserved, as seen in figures on the right.[30][33] Some of these conserved amino acids are part of α-helices in the cytoplasmic and extracellular regions.[30][33]

File:TMEM89 Multiple Sequences Alignment.png
Human TMEM89 Orthologs Multiple Sequence Alignment[30][33]

References

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