TMEM39B

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TMEM39B
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Transmembrane protein 39B (TMEM39B) is a protein that in humans is encoded by the gene TMEM39B. [1] TMEM39B is a multi-pass membrane protein with eight transmembrane domains. [1] The protein localizes to the plasma membrane and vesicles. [1] [2] 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. [3] [4] Furthermore, the TMEM39B protein been found to interact with the SARS-CoV-2 ORF9C (also known as ORF14) protein. [5] 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. [6] [7]

Contents

Gene

The TMEM39B gene in humans is located on the plus strand at 1p35.2. [1] The gene is composed of 14 exons and covers 30.8 kb, spanning from 32,072,031 to 32,102,866. [1] It is flanked by KHDRBS1 upstream and KPNA6 downstream. [1] The TMEM39B gene region also contains the microRNA-encoding gene MIR5585. [1]

Transcript

There are four validated transcript variants for TMEM39B produced by different promoters and alternative splicing. [1] Transcript variant 1 is translated into the longest and most abundant protein isoform.

Transcript Variants of TMEM39B [1]
Transcript variantRefSeq AccessionLength (bp)DescriptionNumber of exons
Transcript variant 1NM_018056.41778 bpEncodes isoform 19
Transcript variant 2 NM_001319677.12106 bpExtended 5' UTR, encodes isoform 29
Transcript variant 3NM_001319678.21542 bpLacks a portion of the 5' coding region, encodes isoform 37
Transcript variant 4NM_001319679.21539 bpLacks a portion of the 5' coding region, encodes isoform 37
Validated transcript variants of TMEM39B, retrieved from AceView. Four validated transcript variants of TMEM39B.png
Validated transcript variants of TMEM39B, retrieved from AceView.

Protein

Isoforms

There are three validated protein isoforms for TMEM39B. [1] Isoform 1 is the longest and the other two isoforms use a downstream in-frame start codon. [1]

Protein Isoforms of TMEM39B
Protein isoformProtein sizeMolecular weightDescription
Isoform 1492 aa56 kDaLongest and most abundant isoform
Isoform 2365 aa42 kDaShorter at N-terminus, uses downstream in-frame start codon
Isoform 3293 aa33 kDaShorter at N-terminus, uses downstream in-frame start codon

General properties

Diagram of TMEM39B topology predicted by Protter. Transmembrane diagram of TMEM39B.png
Diagram of TMEM39B topology predicted by Protter.

The human TMEM39B protein isoform 1 is composed of 492 amino acids and has a predicted molecular weight of 56 kDa. [1] The basal isoelectric point (pI) of the protein is 9.51. [10] Compared to the composition of the human proteome, TMEM39B has a higher percentage of serine, histidine, and leucine and a lower percentage of glutamate and aspartate, making it basic overall. [11] It contains two pairs of tandem repeats: “GSSG” from amino acids 21–28 and “PPSH” from amino acids 107–114. [11] There is a periodic motif of four leucines spaced seven residues apart from amino acids 168–195, which is not predicted to form a leucine zipper. There is an “F..Y” motif with three repeats from amino acids 183-202 and a motif of phenylalanine at every other residue from amino acids 409–416. [11] There are no notable charge clusters, charge runs, or spacings, nor are there any sorting signals. [11]

Topology

TMEM39B isoform 1 contains eight transmembrane regions, and the N-terminus and C-terminus are predicted to be located in the cytosol. [9]

Regulation

Gene-level regulation

Promoter

Promoters for TMEM39B. Promoters of TMEM39B.png
Promoters for TMEM39B.

TMEM39B has several promoter regions predicted by GenoMatix ElDorado. [12] Most promoters are overlapping in a similar region, where use of a different promoter would only cause skipping of the first exon.

Transcription factors

The promoter of TMEM39B transcript variant 1 contains numerous transcription factor binding sites. The transcription factors SMARCA3, TLX1, and CMYB have binding sites with high affinity near the binding site of transcription factor IIB, so they are potential regulators of gene transcription.

TMEM39B Transcription Factors.
Transcription factorDescriptionMatrix similarity
TCF11TCF11/LCR-F1/Nrf1 homodimers1
TFIIBTranscription factor II B (TFIIB) recognition element1
ETV1Ets variant 10.996
ZNF300KRAB-containing zinc finger protein 3000.994
CMYBc-Myb, important in hematopoesis, cellular equivalent to avian myoblastosis virus oncogene v-myb0.994
ASCL1Achaete-scute family bHLH transcription factor 10.99
OSR2Odd-skipped related 20.99
E2F1E2F transcription factor 10.989
ZNF35Human zinc finger protein ZNF350.986
GKLFGut-enriched Krueppel-like factor0.981
PURALPHAPurine-rich element binding protein A0.974
SMARCA3SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 30.973
NFATNuclear factor of activated T-cells0.971
ZF5Zinc finger / POZ domain transcription factor0.962
INSM1Zinc finger protein insulinoma-associated 1 (IA-1)0.958
ZBTB14Zinc finger and BTB domain containing 14 (ZFP-5, ZFP161)0.914
KLF6Core promoter-binding protein (CPBP) with 3 Krueppel-type zinc fingers (KLF6, ZF9)0.891
GABPAGA binding protein transcription factor, alpha0.891
TLX1T-cell leukemia homeobox 10.873
ZNF704Zinc finger protein 7040.847

Expression pattern

RNA sequencing data show that TMEM39B is expressed in all tissues types, with higher levels in the testis, placenta, white blood cells, adrenal gland, thymus, and fetal brain. [6] [7] Microarray data show that TMEM39B is expressed at moderate levels in most tissues, on average in the 58th percentile of genes expressed in a given tissue sample. [13] By percentile rank, TMEM39B is most highly expressed with respect to other genes in BDCA4+ dendritic cells, CD19+ B-cells, and CD14+ monocytes. [13]

Transcript-level regulation

miRNA binding sites

The 3' UTR of the TMEM39B protein contains binding sites for the miRNAs miR-1290, miR-4450, and miRNA-520d-5p. [14] Binding of these miRNAs may lead to RNA silencing.

5' UTR of TMEM39B transcript variant 1. Structure generated by Mfold. 5' UTR of TMEM39B.png
5' UTR of TMEM39B transcript variant 1. Structure generated by Mfold.
3' UTR of TMEM39B transcript variant 1. Structure generated by Mfold. 3' UTR of TMEM39B transcript variant 1.png
3' UTR of TMEM39B transcript variant 1. Structure generated by Mfold.

mRNA-binding proteins

The RNA-binding proteins SFRS13A, ELAVL1, and KHDRBS3 have binding sites in the 3' UTR, and the proteins KHSRP, SFRS9 and YBX1 have binding sites in the 5' UTR. [16] [17]

Secondary structure

The predicted secondary structure of the 5' and 3' UTR of TMEM39B contains multiple stem-loops which may play a role in stability and binding. [15]

Protein-level regulation

Post-translational modifications

Conceptual translation of TMEM39B transcript variant 1. Conceptual translation of Homo sapiens TMEM39B.pdf
Conceptual translation of TMEM39B transcript variant 1.

The TMEM39B protein contains numerous sites of predicted post-translational modifications, including phosphorylation, SUMOylation, acetylation, and glycosylation. [18] [19] [20] [21] [22] [23] [24] Sites of predicted S-palmitoylation at Cys13, Cys87, and Cys264 are conserved in orthologs. SUMOylation is predicted at Lys279 and Lys359. Several well-conserved sites of phosphorylation, glycation, and O-linked-N-acetylglucosaminylation are predicted in cytosolic regions of the protein, as annotated on the conceptual translation of TMEM39B transcript variant 1.

Sub-cellular localization

The TMEM39B protein has been found to localize to the vesicles using immunohistochemistry. [2]

Homology and Evolution

Paralogs

The human TMEM39B gene has a paralog called TMEM39A, also referred to by the alias SUSR2 (suppressor of SQST-1 aggregates in rpl-43 mutants), which is located at 3q13.33. [25] The TMEM39A protein contains 488 amino acids and shares 51.2% identity with TMEM39B. [26] Although the function of the paralog TMEM39A is not well-understood, variants are associated with greater risk of autoimmune disease. [27] The paralog TMEM39A has also been found to interact with Encephalomyocarditis virus (EMCV) capsid proteins as a regulator of the viral autophagy pathway. [28]

Orthologs

TMEM39B has orthologs in species as distant as cartilaginous fish. [26] Mammalian orthologs are highly similar to human TMEM39B, with percent identity greater than 85%. In orthologs in birds, reptiles, and amphibians, the percent identity to human TMEM39B ranges between 70% and 85%. In fish, the percent identity ranges from 40% to 75%. TMEM39B is only conserved in vertebrates, but the paralog TMEM39A has orthologs in species as distant as arthropods. [26] A selected list of orthologs from NCBI BLAST is displayed below. [26]

TMEM39B Orthologs [26]
Genus and SpeciesCommon nameTaxonomic groupDate of divergence (MYA) from humans [29] Accession #Sequence length (aa)Sequence identity to human proteinSequence similarity to human protein
Homo sapiensHumanMammalia0NP_060526.2492100100
Mus musculusHouse mouseMammalia89NP_955009.149296.198
Ornithorhynchus anatinusPlatypusMammalia180XP_028937398.148985.890.5
Gallus gallusRed junglefowlAves318NP_001006313.24898591.5
Thamnophis elegansWestern terrestrial garter snakeReptilia318XP_032083369.149181.588.5
Xenopus tropicalisWestern clawed frogAmphibia352NP_001005048.148375.283.2
Oryzias latipesJapanese medakaActinopterygii433XP_004082414.148874.385.2
Danio rerioZebrafishActinopterygii433NP_956154.149174.284.9
Erpetoichthys calabaricusReedfishActinopterygii433XP_028675900.148971.884.6
Callorhinchus miliiAustralian ghostsharkChondrichthyes465XP_007902480.14907385.1
Amblyraja radiataThorny skateChondrichthyes465XP_032900681.150470.583.5
Scyliorhinus torazameCloudy catsharkChondrichthyes465GCB75241.137355.565.4

Evolution

The TMEM39B gene appears most distantly in cartilaginous fish (chondrichthyes), which diverged from humans approximately 465 million years ago. [29] Orthologs of the paralog TMEM39A are found in arthropods, which diverged from humans approximately 763 million years ago, suggesting that TMEM39B was produced by the duplication of an ancestral form of TMEM39A . [29]

TMEM39B evolves at a relatively slow rate; a 1% change in the amino acid sequence requires approximately 13.9 million years. Based on sequence similarity of orthologs, TMEM39B evolves approximately 1.5 times faster than cytochrome c and 7 times slower than fibrinogen alpha.

Interacting proteins

Immune proteins

Using co-immunoprecipitation, affinity capture MS, and two-hybrid screens, the TMEM39B protein has been found to interact with various membrane glycoproteins . [30] [31] [32] Many interacting proteins have immune functions, including IL13RA1 (interleukin-13 receptor subunit alpha-1), KLRD1 (killer cell lectin-like receptor subfamily D, member 1), and SEMA7A (semaphorin-7A). SEMA7A acts as an activator of T cells and monocytes, while KLDR1 encodes an antigen presented on natural killer cells. [33] [34] IL13RA1 has been proposed to mediate JAK-STAT signaling, which regulates immune cell activation. [35]

SARS-CoV-2

The TMEM39B protein interacts with the SARS-CoV-2 ORF9c accessory protein, also sometimes referred to as ORF14. [5] [36] ORF9C is located within the nucleocapsid (N) gene, overlapping with ORF9b. [36] Two mutations in OFC9c resulting in premature stop codons have been observed in SARS-CoV-2 isolates, suggesting that this reading frame is dispensable for viral replication. [37] The ORF9c protein has been shown to localize to vesicles when transfected into HeLa cells and is predicted to have a non-cytoplasmic domain and transmembrane domain. [38]

Variants

Many SNPs (single nucleotide polymorphisms) have been detected in the TMEM39B gene, of which a smaller subset cause nonsynonymous amino acid changes. [39] There are notably fewer SNPs that occur at sites of post-translational modifications, motifs, or highly conserved amino acids; changes in these amino acids may be more likely to have phenotypic effects. The table below lists selected SNPs resulting in a change at such sites.

Selected SNPs in TMEM39B [39]
SNPmRNA positionBase changeAmino acid positionAmino acid changeDescription
rs1259613993180C > T11S > P“GSSG” repeat
rs1446462546271C > T41S > FO-GlcNAc, phosphorylation site
rs867417059282A > T45S > CO-GlcNAc, phosphorylation site
rs1009960963289C > T47S > FPhosphorylation site
rs377359320503C > A118N > KHighly conserved
rs748779192555C > T136R > CHighly conserved
rs778604874558C > T137R > CHighly conserved
rs1419668726696T > C183F > L[F..Y] motif
rs759591458963C > T272R > CHighly conserved
rs11806953321003G > C285R > PHighly conserved
rs2000481801009A > G287K > RGlycation site
rs14452261081060C > T304P > LHighly conserved
rs7717439351206C > A353H > NHighly conserved
rs3762578491294G > A382G > DHighly conserved
rs13687704551302G > T385V > LHighly conserved
rs7561068661336G > A396G > DHighly conserved
rs8687211121356C > T403P > SHighly conserved
rs13838032941369C > G407S > CPhosphorylation site
rs9170857321581T > G478S > AO-GlcNAc, phosphorylation site

Clinical significance

In a study using 164 tumor samples from patients with diffuse large B cell lymphoma, TMEM39B was one of 17 genes identified as part of a prognostic profile for 5-year progression-free survival. [3] In another study using a genome-wide siRNA screen, knockdown of TMEM39B with siRNAs decreased viral capsid/autophagosome colocalization, survival of virus-infected cells, and mitophagy in HeLa cells infected with Sindbis virus. [4] This may suggest that TMEM39B plays a role in viral autophagy like its paralog TMEM39A.

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References

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