TMEM169

The gene is located on human chromosome 2(2q35) and spans 20,918 bases (216,081,866-216,102,783){{Cite web|title=TMEM169 Gene - GeneCards {{!}} TM169 Protein {{!}} TM169 Antibody|url=https://www.genecards.org/cgi-bin/carddisp.pl?gene=TMEM169&keywords=TMEM169|access-date=2020-09-29|website=www.genecards.org}} on the + strand. The gene contains four exons in total. The direct neighbors of TMEM169 include XRCC5 (X-ray repair cross complementing 5) and PECR (peroxisomal trans-2-enoyl-CoA reductase).

Transcription of TMEM169 gene produces five alternatively spliced variants to generate four variants of the transcript. The variants all code for the same protein and have differences within the 5’ UTR region. Variant 1 is the longest transcript (NM_001142310.2) and consists of 3,408 base pairs and four exons.

All four transcripts encode for the same protein (TMEM169) consisting of 297 amino acids. According to SAPS{{Cite web|title=SAPS < Sequence Statistics < EMBL-EBI|url=https://www.ebi.ac.uk/Tools/seqstats/saps/|access-date=2020-12-16|website=www.ebi.ac.uk}} the molecular weight of protein TMEM169 is 33.6 kdal and it has an overall net negative charge (-5.7%). TMEM169 has an isoelectric point of 4.76.{{Cite web|title=SIB Swiss Institute of Bioinformatics {{!}} Expasy|url=https://www.expasy.org/|access-date=2020-12-16|website=www.expasy.org}}

There are two transmembrane domains of Homo sapiens TMEM169 located at amino acids 160-180 and 211-231. The N and C terminus are both located in the cytoplasmic domain.{{Cite web|title=Phyre 2 alignment of Undefined with c5doqC_|url=http://www.sbg.bio.ic.ac.uk/phyre2/phyre2_output/46c1604c047fd805/aligs/c5doqC_.1.alig.html|access-date=2020-12-18|website=www.sbg.bio.ic.ac.uk}} The conceptual translation provides further annotation of Homo sapiens TMEM169 protein.

The specific structure of TMEM169 is unknown, although includes both alpha helices and beta sheets.{{Cite web|title=Phyre 2 alignment of Undefined with c5doqC_|url=http://www.sbg.bio.ic.ac.uk/phyre2/phyre2_output/46c1604c047fd805/aligs/c5doqC_.1.alig.html|access-date=2020-12-16|website=www.sbg.bio.ic.ac.uk}}

518x518pxFile:Conceptually Translated TMEM169 Wiki (2).pdf

The promoter (GXP_6745619) is 1242 base pairs at coordinates 216080866-216082107. It supports 11 coding transcripts.

File:Promoter_of_TMEM169.png

Table 2. There are four promoters that result from TMEM169 search on Genomatix.{{Cite web|title=Genomatix Software Suite - Scientific Analysis of genomic data|url=https://www.genomatix.de/solutions/genomatix-software-suite.html|access-date=2020-12-07|website=www.genomatix.de|archive-date=2012-01-14|archive-url=https://web.archive.org/web/20120114124429/http://www.genomatix.de/solutions/genomatix-software-suite.html|url-status=dead}}

RNA sequencing data revealed TMEM169 is expressed ubiquitously, although it displays high expression in the brain, particularly during fetal development. HPA RNA-seq normal tissues for TMEM169 were obtained from 95 human tissue samples. The HPA RNA-seq demonstrates highest expression of TMEM169 in the brain (RPKM=3.159). Particularly, in the fetal brain (RPKM= 1.583) and cerebellum(RPKM=0.795).

GEO Profile: GDS3113/220527{{Cite web|title=49003965 - GEO Profiles - NCBI|url=https://www.ncbi.nlm.nih.gov/geoprofiles/49003965|access-date=2020-12-07|website=www.ncbi.nlm.nih.gov}}

The highest expression of TMEM169 is found in the fetal brain. TMEM169 tends to have a high expression in the brain relative to other tissues, although not to other genes.

The use of polyclonal TMEM169 antibody (NBP2-69796) of a human melanoma cell line (SK-MEL-30) in the host of rabbit demonstrates TMEM169 localization to nucleoplasm, cytosol and centrosome.{{Cite web|title=TMEM169 Antibodies|url=https://www.novusbio.com/primary-antibodies/tmem169|access-date=2020-12-07|website=Novus Biologicals}} Strong positivity in glial cells is revealed through immunohistochemical staining of the human cerebral cortex with antibody HPA074877.{{Cite web|title=Tissue expression of TMEM169 - Staining in cerebral cortex - The Human Protein Atlas|url=https://www.proteinatlas.org/ENSG00000163449-TMEM169/tissue/cerebral+cortex#imid_1408|access-date=2020-12-07|website=www.proteinatlas.org}}

File:Protein Diagram .png

The MyHits{{Cite web|title=Motif Scan|url=https://myhits.sib.swiss/cgi-bin/motif_scan|access-date=2020-12-16|website=myhits.sib.swiss|language=en}} Tool revealed two types of conserved predicted post-translational modifications.

TMEM169 is well-conserved across strict orthologs shown by the following multiple sequence alignment created Clustal{{Cite web|title=Clustal Omega < Multiple Sequence Alignment < EMBL-EBI|url=https://www.ebi.ac.uk/Tools/msa/clustalo/|access-date=2020-10-29|website=www.ebi.ac.uk}} using BoxShade.{{Cite web|title=BoxShade Server|url=https://embnet.vital-it.ch/software/BOX_form.html|access-date=2020-10-29|website=embnet.vital-it.ch|archive-date=2020-10-29|archive-url=https://web.archive.org/web/20201029051832/https://embnet.vital-it.ch/software/BOX_form.html|url-status=dead}} The multiple sequence alignment of distant orthologs highlighting the transmembrane domains was also created using Clustal and BoxShade. The red boxes illustrate conserved transmembrane domains across orthologs. File:STRICTMSA NEW.jpg

Orthologs are found in over 300 organisms within the kingdom metazoan. There are not any orthologs found in fungi or plants. Invertebrates are the most distantly related orthologs, according to BLAST searches. The subset of closely related organisms include mammals, reptiles, birds, and amphibians (E-value 1e-177 to 1e-124). These orthologs range from 78% to 93% sequence similarity to the human protein. Moderately related orthologs to human TMEM169 protein include fish and cephalochordates (similarity= 62%-75%; E-value= 3e-120 to 1e-71). Protein sequences of hemichordates, arthropods, and mollusks are the most distantly related to the human protein sequence (similarity= 56%-64%; E-value= 2e-58 to 1e-44).{{Cite web|title=BLAST: Basic Local Alignment Search Tool|url=https://blast.ncbi.nlm.nih.gov/Blast.cgi|access-date=2020-10-22|website=blast.ncbi.nlm.nih.gov}} The most distantly related organism with TMEM169 ortholog is Anopheles albimanus, within the taxonomic group Arthropoda. The size of the gene family for Anopheles albimanus is one and there is only one isoform.{{Cite web|title=transmembrane protein 169-like [Anopheles albimanus] - Protein - NCBI|url=https://www.ncbi.nlm.nih.gov/protein/XP_035794912.1?report=genbank&log$=protalign&blast_rank=2&RID=RRR144DT01R|access-date=2020-10-22|website=www.ncbi.nlm.nih.gov}}

File:Distant Orthologs MSA TMEM Domain.png

File:Rate_of_divergence.png

Table 1. Identified orthologs of Homo sapiens TMEM169 protein. The table is organized by increasing DOD (data of divergence from the human lineage) and then by sequence similarity to the human protein (%). The date of divergence was calculated using TimeTree.{{Cite web|title=TimeTree :: The Timescale of Life|url=http://www.timetree.org|access-date=2020-10-29|website=www.timetree.org}} Seq. is an abbreviation for sequence.

TMEM169 gene first appeared in invertebrates, more specifically in arthropods and mollusks. The approximate date of divergence from humans for arthropods and mollusks is 797 million years ago (MYA).{{Cite web|title=TimeTree :: The Timescale of Life|url=http://www.timetree.org/|access-date=2020-10-22|website=www.timetree.org}} Based upon comparison of the evolution for cytochrome C (a quickly evolving protein) and fibrinogen alpha chain (a slowly evolving protein), TMEM169 gene is evolving at a moderate pace.

RhoU (rho-related GTP-binding protein RhoU) is known to interact with TMEM169 according to PSICQUIC.{{Cite web|title=PSICQUIC View|url=http://www.ebi.ac.uk/Tools/webservices/psicquic/view/results.xhtml?conversationContext=1|access-date=2020-12-16|website=www.ebi.ac.uk}} The pull down assay revealed RhoU as a protein interaction with TMEM169.{{cite journal | vauthors = Dart AE, Box GM, Court W, Gale ME, Brown JP, Pinder SE, Eccles SA, Wells CM | display-authors = 6 | title = PAK4 promotes kinase-independent stabilization of RhoU to modulate cell adhesion | journal = The Journal of Cell Biology | volume = 211 | issue = 4 | pages = 863–79 | date = November 2015 | pmid = 26598620 | pmc = 4657161 | doi = 10.1083/jcb.201501072 }}

A single nucleotide polymorphism of TMEM169, defined as rs3821104, is one of two SNP’s that revealed strong association (p<0.1) with Chronic Obstructive Pulmonary Disease (COPD) within the international COPD genetics network.{{cite journal | vauthors = Hersh CP, Pillai SG, Zhu G, Lomas DA, Bakke P, Gulsvik A, DeMeo DL, Klanderman BJ, Lazarus R, Litonjua AA, Sparrow D, Reilly JJ, Agusti A, Calverley PM, Donner CF, Levy RD, Make BJ, Paré PD, Rennard SI, Vestbo J, Wouters EF, Scholand MB, Coon H, Hoidal J, Silverman EK | display-authors = 6 | title = Multistudy fine mapping of chromosome 2q identifies XRCC5 as a chronic obstructive pulmonary disease susceptibility gene | journal = American Journal of Respiratory and Critical Care Medicine | volume = 182 | issue = 5 | pages = 605–13 | date = September 2010 | pmid = 20463177 | pmc = 2937234 | doi = 10.1164/rccm.200910-1586OC }} Additionally, gene TMEM169 is one of the four most down-regulated genes in response to oxidative stress; it is downregulated by 0.50 fold in patients with myocardial infarctions.{{cite journal | vauthors = Yue X, Acun A, Zorlutuna P | title = Transcriptome profiling of 3D co-cultured cardiomyocytes and endothelial cells under oxidative stress using a photocrosslinkable hydrogel system | journal = Acta Biomaterialia | volume = 58 | pages = 337–348 | date = August 2017 | pmid = 28648749 | pmc = 5563470 | doi = 10.1016/j.actbio.2017.06.031 }} The gene has association to two different birth defects; neural tube defects and preeclampsia. An amino acid change (p.K41I) in TMEM169 is known to cause neural tube defects{{cite journal | vauthors = Pappa L, Kals M, Kivistik PA, Metspalu A, Paal A, Nikopensius T | title = Exome analysis in an Estonian multiplex family with neural tube defects-a case report | journal = Child's Nervous System | volume = 33 | issue = 9 | pages = 1575–1581 | date = September 2017 | pmid = 28721594 | doi = 10.1007/s00381-017-3491-1 | s2cid = 25442338 }} and hypermethylated loci cg20968678, associated with TMEM169, leads to early onset preeclampsia.{{cite journal | vauthors = Ching T, Ha J, Song MA, Tiirikainen M, Molnar J, Berry MJ, Towner D, Garmire LX | display-authors = 6 | title = Genome-scale hypomethylation in the cord blood DNAs associated with early onset preeclampsia | journal = Clinical Epigenetics | volume = 7 | issue = 1 | pages = 21 | date = 2015-03-13 | pmid = 25806090 | pmc = 4371797 | doi = 10.1186/s13148-015-0052-x | doi-access = free }}

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